Multiple antigen binding molecular fusion, pharmaceutical composition, method for identifying linear epitope, and method for preparing multiple antigen binding molecular fusion

ABSTRACT

A multiple antigen-binding molecule fusion molecule containing a multiple antigen-binding molecule (α) having an immune cell antigen-binding region and a cancer antigen-binding region, a cancer tissue-specific protease-cleavable linker (β), and a masking molecule (γ) containing a polypeptide having the amino acid sequence QDGNE, in which the multiple antigen-binding molecule (α) and the masking molecule (γ) are linked via the cancer tissue-specific protease-cleavable linker (β).

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a U.S. National Phase of International Patent Application No. PCT/JP2016/064301, filed May 13, 2016, which claims priority to Japanese Patent Application No. 2015-098208, filed May 13, 2015, each of which is incorporated herein by reference.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing (Name: 6663_0050_Sequence_Listing.txt; Size: 279,365 bytes; and Date of Creation: Nov. 2, 2017) filed with the application is incorporated herein by reference in its entirety.

TECHNICAL FIELD

The present invention relates to multiple antigen-binding molecule fusion molecules, pharmaceutical compositions, methods for identifying linear epitopes, and methods for producing multiple antigen-binding molecule fusion molecules.

BACKGROUND ART

Antibodies are drawing attention as pharmaceuticals as they are highly stable in plasma and have few side effects. In particular, a number of IgG-type antibody pharmaceuticals are available on the market, and many antibody pharmaceuticals are currently under development (Non-Patent Documents 1 and 2).

As cancer therapeutic agents using antibody pharmaceuticals, Rituxan (registered trademark) against a CD20 antigen, cetuximab against an EGFR antigen, herceptin (registered trademark) against a HER2 antigen, and such have been approved so far (Non-Patent Document 3). These antibody molecules bind to antigens expressed on cancer cells, and exhibit cytotoxic activity against cancer cells by ADCC and such. Such cytotoxic activity by ADCC and etc. are known to depend on the number of antigens expressed on cells targeted by the therapeutic antibodies (Non-Patent Document 4); therefore, high expression level of the target antigen is preferable from the stand point of the effects of the therapeutic antibodies. However, even if the antigen expression level is high, when antigens are expressed in normal tissues, cytotoxic activity mediated by ADCC etc. will be exerted against normal cells, and therefore side-effects will become a major problem. Therefore, antigens targeted by therapeutic antibodies used as therapeutic agents for cancer are preferably antigens specifically expressed in cancer cells. For example, antibody molecules against the EpCAM antigen which is known as a cancer antigen have been considered to be promising as therapeutic agents for cancer. However, the EpCAM antigen is known to be expressed in the pancreas as well, and in practice, administration of anti-EpCAM antibodies in clinical trials has been reported to cause pancreatitis as a side-effect due to cytotoxic activity towards the pancreas (Non-Patent Document 5).

Following the success of antibody pharmaceuticals that exert cytotoxic activity by ADCC activity, a second generation of improved antibody molecules that exert strong cytotoxic activity through enhancement of ADCC activity by removing fucose of N-type sugar chains in the native human IgG1 Fc region (Non-Patent Document 6), enhancement of ADCC activity by enhancing the binding toward Fcγ receptor IIIa by substitution of amino acids in the native human IgG1 Fc region (Non-Patent Document 7), and such have been reported. As antibody pharmaceuticals that exert cytotoxic activity against cancer cells through a mechanism other than the above-mentioned ADCC activity mediated by NK cells, improved antibody molecules that exert a stronger cytotoxic activity, such as an antibody-drug conjugate (ADC) in which an antibody is conjugated with a drug having potent cytotoxic activity (Non-Patent Document 8), and a low molecular weight antibody that exerts toxic activity against cancer cells by recruiting T cells to cancer cells (Non-Patent Document 9), have been reported as well.

Such antibody molecules exerting a stronger cytotoxic activity can exert cytotoxic activity against cancer cells that do not have much antigen expression, but on the other hand, they will exert similar cytotoxic activity against normal tissues with low antigen expression. In fact, in comparison to cetuximab which is a natural human IgG1 against EGFR, EGFR-BiTE, which is a bispecific antibody against CD3 and EGFR, can exert a potent cytotoxic activity against cancer cells by recruiting T cells to cancer cells and exert antitumor effects. On the other hand, since EGFR is expressed also in normal tissues, when EGFR-BiTE is administered to cynomolgus monkeys, serious side effects have appeared (Non-Patent Document 10). Furthermore, bivatuzumab mertansine, an ADC formed by linking mertansine to an antibody against CD44v6 which is highly expressed in cancer cells, has been shown to cause severe skin toxicity and liver toxicity in clinical practice because CD44v6 is expressed also in normal tissues (Non-Patent Document 11).

When antibodies that can exert a potent cytotoxic activity against cancer cells having low antigen expression are used as such, the target antigen needs to be expressed in a highly cancer-specific manner. However, since HER2 and EGFR, which are target antigens of herceptin (registered trademark) and cetuximab, respectively, are also expressed in normal tissues, the number of cancer antigens expressed in a highly cancer-specific manner is thought to be limited. Therefore, while it is possible to strengthen the cytotoxic activity against cancer, the side effects occurring due to cytotoxic actions against normal tissues may become problematic.

Furthermore, recently, ipilimumab which enhances tumor immunity by inhibiting CTLA4 which contributes to immunosuppression in cancer was shown to prolong overall survival of metastatic melanoma (Non-Patent Document 12). However, since ipilimumab inhibits CTLA4 systemically, while tumor immunity is enhanced, the emergence of autoimmune disease-like severe side effects due to systemic activation of the immune system is becoming a problem (Non-Patent Document 13).

On the other hand, as antibody pharmaceuticals against diseases besides cancer, antibody pharmaceuticals that exert therapeutic effects by inhibiting inflammatory cytokines in inflammatory/autoimmune diseases are known (Non-Patent Document 14). For example, Remicade (registered trademark) and Humira (registered trademark) which target TNF, and Actemra (registered trademark) which targets the IL-6 receptor exhibit high therapeutic effects against rheumatoid arthritis, but on the other hand, systemic neutralization of these cytokines has led to the observation of infection as side effects (Non-Patent Document 15).

Various techniques have been developed as techniques that can be applied to second-generation antibody pharmaceuticals. While techniques for improving effector functions, antigen-binding ability, pharmacokinetics, and stability, or techniques for reducing immunogenic risks have been reported (Non-Patent Document 16), there are hardly any reports on techniques that enable target tissue-specific action of antibody pharmaceuticals to overcome such side effects. For example, regarding lesions such as cancer tissues and inflammatory tissues, pH-dependent antibodies that make use of the acidic pH condition at these target tissues have been reported (Patent Documents 1 and 2). However, the decrease of pH (that is, increase in hydrogen ion concentration) in cancer tissues and inflammatory tissues as compared to normal tissues is slight, and since it is difficult to produce antibodies that act by detecting a slight increase in the concentration of hydrogen ions which have an extremely small molecular weight, and also because acidic pH conditions may be found in normal tissues such as osteoclastic bone resorption region or in tissues other than the lesion of interest, use of pH conditions as a lesion-specific environmental factor was considered to face many challenges.

On the other hand, methods for producing antibodies that exert antigen-binding activity only after they are cleaved by a protease expressed at lesion sites such as cancer tissues and inflammatory tissues have been reported (Patent Documents 3 and 4). In these methods, an artificial peptide having binding activity to an antigen-binding site of an antibody against a target antigen is fused to an antibody via a linker which can be cleaved by a protease, so that, when the linker is cleaved by a protease, the artificial peptide dissociates from the antibody and binding to the target antigen is enabled.

Furthermore, molecules in which a CD3ε partial protein is linked to an anti-CD3ε antibody (OKT3) via a linker to mask the CD3ε-binding activity, which is recovered by cleavage of the linker by a protease, have been reported (Patent Document 5).

PRIOR ART DOCUMENTS Patent Documents

-   [Patent Document 1] WO 2003/105757 -   [Patent Document 2] WO 2012/033953 -   [Patent Document 3] WO 2010/081173 -   [Patent Document 4] WO 2009/025846 -   [Patent Document 5] WO 2013/128194

Non-Patent Documents

-   [Non-Patent Document 1] Janice M Reichert, Clark J Rosensweig, et     al., ‘Monoclonal antibody successes in the clinic.’ Nat.     Biotechnol., 2005, Vol. 23, pp. 1073-1078. -   [Non-Patent Document 2] Pavlou A K, Belsey M J., ‘The therapeutic     antibodies market to 2008’, Eur. J. Pharm. Biopharm., 2005, Vol. 59,     No. 3, pp. 389-396. -   [Non-Patent Document 3] Weiner L M, Surana R, et al., ‘Monoclonal     antibodies: versatile platforms for cancer immunotherapy’, Nat. Rev.     Immunol., 2010, Vol. 10, No. 5, pp. 317-327. -   [Non-Patent Document 4] Lewis G D, Figari I, et al., ‘Differential     responses of human tumor cell lines to anti-pi 85HER2 monoclonal     antibodies’, Cancer Immunol. Immunotherapy, 1993, Vol. 37, pp.     255-263. -   [Non-Patent Document 5] de Bono J S, Tolcher A W, et al., ‘ING-1, a     monoclonal antibody targeting Ep-CAM in patients with advanced     adenocarcinomas’, Clin. Cancer Res., 2004, Vol. 10, No. 22, pp.     7555-7565. -   [Non-Patent Document 6] Satoh M, Iida S, et al., ‘Non-fucosylated     therapeutic antibodies as next-generation therapeutic antibodies’,     Expert Opin. Biol. Ther., 2006, Vol. 6, No. 11, pp.1161-1173. -   [Non-Patent Document 7] Desjarlais J R, Lazar G A, et al.,     ‘Optimizing engagement of the immune system by anti-tumor     antibodies: an engineer's perspective’, Drug Discov. Today, 2007,     Vol. 12, No. 21-22, pp. 898-910. -   [Non-Patent Document 8] Alley S C, Okeley N M, et al.,     ‘Antibody-drug conjugates: targeted drug delivery for cancer’, Curr.     Opin. Chem. Biol., 2010, Vol. 14, No. 4, pp. 529-537. -   [Non-Patent Document 9] Baeuerle P A, Kufer P, et al., ‘BiTE:     Teaching antibodies to engage T-cells for cancer therapy’, Curr.     Opin. Mol. Ther., 2009, Vol. 11, No. 1, pp. 22-30. -   [Non-Patent Document 10] Lutterbuese R, Raum T, et al., ‘T     cell-engaging BiTE antibodies specific for EGFR potently eliminate     KRAS- and BRAF-mutated colorectal cancer cells’, Proc. Natl. Acad.     Sci. U.S.A., 2010, Vol. 107, No. 28, pp. 12605-12610. -   [Non-Patent Document 11] Riechelmann H, Sauter A, et al., ‘Phase I     trial with the CD44v6-targeting immunoconjugate bivatuzumab     mertansine in head and neck squamous cell carcinoma’, Oral Oncol.,     2008, Vol. 44, No. 9, pp.823-829. -   [Non-Patent Document 12] Trinh V A, Hwu W J., ‘Ipilimumab in the     treatment of melanoma’, Expert Opin. Biol. Ther., 2012, Apr., 14     (doi: 10.1517/14712598.2012.675325). -   [Non-Patent Document 13] Juszczak A, Gupta A, et al., ‘IPILIMUMAB—A     NOVEL IMMUNOMODULATING THERAPY CAUSING AUTOIMMUNE HYPOPHYSITIS: A     CASE REPORT AND REVIEW’ Eur. J. Endocrinol., 2012, April, 10 (doi:     10.1530/EJE-12-0167). -   [Non-Patent Document 14] Takeuchi T, Kameda H., ‘The Japanese     experience with biologic therapies for rheumatoid arthritis’, Nat.     Rev. Rheumatol., 2010, Vol. 6, No. 11, pp. 644-652. -   [Non-Patent Document 15] Nam J L, Winthrop K L, et al., ‘Current     evidence for the management of rheumatoid arthritis with biological     disease-modifying antirheumatic drugs: a systematic literature     review informing the EULAR recommendations for the management of     RA’, Ann. Rheum. Dis., 2010 Vol. 69, No. 6, pp. 976-986. -   [Non-Patent Document 16] Kim S J, Park Y, et al., ‘Antibody     engineering for the development of therapeutic antibodies’, Mol.     Cells., 2005, Vol. 20, No. 1, pp. 17-29.

SUMMARY OF THE INVENTION Problems to be Solved by the Invention

An objective of the present invention is to generate and provide derivatives (herein, also referred to as “multiple antigen-binding molecule fusion molecules”) for generically producing multiple antigen-binding molecules (also called “multispecific antigen-binding molecules”) which recognize cancer antigens and CD3 and have reduced side-effects. Further, another objective is to provide pharmaceutical compositions containing multiple antigen-binding molecule fusion molecules; methods for identifying linear epitopes that are useful for multiple antigen-binding molecule fusion molecules; and methods for producing multiple antigen-binding molecule fusion molecules.

Means for Solving the Problems

As a result of dedicated research to accomplish the above-mentioned objectives, the present inventors generated multiple antigen-binding molecule fusion molecules that recognize a cancer antigen and CD3, whose CD3-binding activity is inhibited by a polypeptide having a specific amino acid sequence. This polypeptide is linked to a multiple antigen-binding molecule by a specific linker, and multiple antigen-binding molecule fusion molecules that exhibit activities specifically in cancer tissues upon cleavage of the linker by a cancer tissue-specific protease, were provided. Furthermore, the present inventors generated methods for identifying linear epitopes that are useful for multiple antigen-binding molecule fusion molecules and methods for producing the multiple antigen-binding molecule fusion molecules, and completed the present invention.

More specifically, the present invention provides the following:

-   [1] a multiple antigen-binding molecule fusion molecule comprising:     -   a multiple antigen-binding molecule (α) which comprises an         immune cell antigen-binding region which recognizes an antigen         that comprises a polypeptide consisting of the amino acid         sequence QDGNE (SEQ ID NO: 15) and a cancer antigen-binding         region which recognizes a cancer antigen;     -   a cancer tissue-specific protease-cleavable linker (β) which         comprises a polypeptide consisting of a target sequence of a         cancer tissue-specific protease; and a masking molecule (γ)         which comprises a polypeptide consisting of the amino acid         sequence QDGNE (SEQ ID NO: 15);     -   wherein the multiple antigen-binding molecule (α) and the         masking molecule (γ) are linked via the cancer tissue-specific         protease-cleavable linker (β); -   [2] the multiple antigen-binding molecule fusion molecule of [1],     wherein the immune cell antigen-binding region recognizes at least     one type of immune cell antigen other than the antigen that     comprises a polypeptide consisting of the amino acid sequence QDGNE     (SEQ ID NO: 15); -   [3] the multiple antigen-binding molecule fusion molecule of [2],     wherein the immune cell antigen-binding region does not recognize     two or more immune cell antigens simultaneously; -   [4] the multiple antigen-binding molecule fusion molecule of any one     of [1] to [3], wherein the multiple antigen-binding molecule (α) is     an antibody or an antibody fragment comprising at least two Fv     regions, and the cancer antigen-binding region and the immune cell     antigen-binding region are formed by different Fv regions; -   [5] the multiple antigen-binding molecule fusion molecule of [4],     wherein light chains of the antibody or the antibody fragment     comprising at least two Fv regions both comprise a same amino acid     sequence; -   [6] the multiple antigen-binding molecule fusion molecule of [4] or     [5], wherein the antibody or antibody fragment comprising at least     two Fv regions further comprises an Fc region, and the Fc region is     modified so as to lack a function of recognizing an Fcγ receptor; -   [7] the multiple antigen-binding molecule fusion molecule of any one     of [4] to [6], wherein the cancer tissue-specific protease-cleavable     linker (β) is fused to a heavy chain N-terminus or a light chain     N-terminus of the Fv region that forms the immune cell     antigen-binding region; -   [8] the multiple antigen-binding molecule fusion molecule of [7],     wherein the cancer tissue-specific protease-cleavable linker (β) and     the masking molecule (γ) form a linear fusion polypeptide, and     wherein     -   the number of amino acids in the fusion polypeptide is eleven or         more to 65 or less when the cancer tissue-specific         protease-cleavable linker (β) is fused to the heavy chain         N-terminus of the Fv region that forms the immune cell         antigen-binding region; and     -   the number of amino acids in the fusion polypeptide is 16 or         more to 65 or less when the cancer tissue-specific         protease-cleavable linker (β) is fused to the light chain N         terminus of the Fv region that forms the immune cell         antigen-binding region; -   [9] the multiple antigen-binding molecule fusion molecule of any one     of [1] to [8], wherein the target sequence is the amino acid     sequence PLGLAG (SEQ ID NO: 9); -   [10] a pharmaceutical composition which comprises the multiple     antigen-binding molecule fusion molecule of any one of [1] to [9]     and a pharmaceutically acceptable carrier; -   [11] the pharmaceutical composition of [10], which is for treating     cancer; -   [12] a method for treating cancer, wherein the method comprises     administering the pharmaceutical composition of [10] or [11] to a     patient; -   [13] a method for identifying a linear epitope, wherein the method     comprises identifying a linear epitope comprised in the immune cell     antigen and recognized by the immune cell antigen-binding region     based on three-dimensional protein structure analysis data obtained     by using a protein complex of an immune cell antigen and an immune     cell antigen-binding region which recognizes the immune cell     antigen; -   [14] a method for producing a multiple antigen-binding molecule     fusion molecule, wherein the method comprises expressing a fusion     protein in which a linear epitope is fused to a multiple     antigen-binding molecule (α) which comprises a cancer     antigen-binding region that recognizes a cancer antigen and an     immune cell antigen-binding region that recognizes an immune cell     antigen via a cancer tissue-specific protease-cleavable linker (β)     which comprises a region that is cleavable by a protease     specifically expressed in a cancer tissue expressing the cancer     antigen; -   [15] the multiple antigen-binding molecule fusion molecule of any     one of [1] to [9] or the pharmaceutical composition of [10] or [11]     for use in treating cancer; -   [16] use of the multiple antigen-binding molecule fusion molecule of     any one of [1] to [9] or the pharmaceutical composition of [10] or     [11] for the manufacture of an anticancer agent; and -   [17] a method for producing an anticancer agent, wherein the method     comprises using the multiple antigen-binding molecule fusion     molecule of any one of [1] to [9] or the pharmaceutical composition     of [10] or [11].

Effects of the Invention

The present invention enables provision of derivatives (multiple antigen-binding molecule fusion molecules) for generically producing multiple antigen-binding molecules which recognize cancer antigens and CD3 and have reduced side-effects, and further provision of pharmaceutical compositions containing the multiple antigen-binding molecule fusion molecules; methods for identifying linear epitopes useful for the multiple antigen-binding molecule fusion molecules; and methods for producing multiple antigen-binding molecule fusion molecules.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows an alignment of the amino acid sequences of human CD3ε (SEQ ID NO: 37) and cynomolgus CD3ε (SEQ ID NO: 38).

FIG. 2 shows an overall conceptual diagram of an embodiment of a multiple antigen-binding molecule fusion molecule of the present invention.

FIG. 3 shows a partial conceptual diagram of another embodiment of a multiple antigen-binding molecule fusion molecule of the present invention. The upper figure shows a heavy-chain N-terminal fusion molecule and the lower figure shows a light-chain N-terminal fusion molecule.

FIG. 4 is a graph showing the results of cellular ELISA for CE115 against CD3ε.

FIG. 5 shows a 2Fo-Fc electron density map of the binding site of an anti-CD3 antibody Fab fragment and an epitope peptide. In the figure, the antibody is indicated by thin lines, and the epitope peptide is indicated by thick lines. Each of the amino acid residues of the epitope peptide from the N-terminus to the fifth amino acid residue is represented by a one-letter amino acid code and the serial number from the N-terminal side. The electron density map is shown as a mesh.

FIGS. 6A-6D show surface representations of models where the epitope core sequence is linked to the N terminus of the antibody heavy chain variable region via a Gly linker. In the figures, the antibody heavy chain is shown in black, the antibody light chain is shown in gray, and the linker is shown by a thick white line. FIG. 6A shows a model where the linkage is made by a linker consisting of six amino acid residues. FIG. 6B shows a model where the linkage is made by a linker consisting of nine amino acid residues. FIG. 6C shows a model where the linkage is made by a linker consisting of twelve amino acid residues. FIG. 6D shows a model where the linkage is made by a linker consisting of 16 amino acid residues.

FIGS. 7-D show surface representations of models where the epitope core sequence is linked to the N terminus of the antibody light chain variable region via a Gly linker. In the figures, the antibody heavy chain is shown in black, the antibody light chain is shown in gray, and the linker is shown by a thick white line. FIG. 7A shows a model where the linkage is made by a linker consisting of eleven amino acid residues. FIG. 7B shows a model where the linkage is made by a linker consisting of twelve amino acid residues. FIG. 7C shows a model where the linkage is made by a linker consisting of 14 amino acid residues. FIG. 7D shows a model where the linkage is made by a linker consisting of 16 amino acid residues.

FIG. 8-1 shows the results of evaluating CD3ε-binding activities of anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease (uPA) treatment. The results are shown as a proportion when defining the luminescence value for a well without antigen addition as 1. (i) shows the CD3ε-binding activities of antibodies with a peptide attached to their heavy chain N-terminus, and (ii) shows the CD3ε-binding activities of antibodies with a peptide attached to their light chain N-terminus.

FIG. 8-2 shows the results of evaluating CD3ε-binding activities of anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease (uPA) treatment. The results are shown as a proportion when defining the luminescence value for a well without antigen addition as 1. (iii) shows, similarly to (ii), the CD3ε-binding activities of antibodies (TWO arm antibodies) with a peptide attached to their light chain N-terminus. (iv) shows the CD3ε-binding activities of antibodies with a peptide attached to the heavy chain N-terminus of AN121.

FIG. 9 shows the results of evaluating CD3ε-binding activities of anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease (human MT-SP1) treatment. The results are shown as a proportion when defining the luminescence value for a well without antigen addition as 1. (i) shows the CD3ε-binding activities of antibodies with a peptide attached to their heavy chain N-terminus, and (ii) shows the CD3ε-binding activities of antibodies with a peptide attached to their light chain N-terminus.

FIG. 10 shows the results of evaluating CD3ε-binding activities of anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease (MMP-2) treatment. The results are shown as a proportion when defining the luminescence value for the antibody at 1 μg/mL as 1. (i) shows the CD3ε-binding activities of antibodies with a peptide attached to their heavy chain N-terminus, and (ii) shows the CD3ε-binding activities of antibodies with a peptide attached to their light chain N-terminus.

FIGS. 11-1 and 11-2 show the results of evaluating CD3ε activation by anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease treatment. The derivatives have been prepared based on an antibody in which the heavy chain is hCE115HA and the light chain is GLS3000. FIG. 11-1 shows the results for an unmodified antibody to which no peptide has been attached and an antibody to which a masking molecule (γ) has been attached using a noncleavable GS linker. FIG. 11-2 shows the results for antibodies to which a masking molecule (γ) has been attached using a cancer tissue-specific protease-cleavable linker (β). The masking molecule (γ) of the respective antibodies is composed of a sequence of seven amino acids (since the linker portion includes a GG sequence, the sequence up to the ninth amino acid is the same sequence as the CD3ε N-terminus), 20 amino acids, or 27 amino acids from the N-terminus of CD3ε. In both FIGS. 11-1 and 11-2, the solid lines indicate protease-treated antibodies and the dashed lines indicate antibodies not subjected to protease treatment.

FIGS. 12-1 and 12-2 show the results of evaluating CD3ε activation by anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease treatment. The derivatives have been prepared based on an antibody in which the light chain is GLS3000 and AN121 having hCE115HA with enhanced CD3ε binding force. FIG. 12-1 shows the results for an unmodified antibody to which no peptide has been attached and antibody to which a masking molecule (γ) has been attached using a noncleavable GS linker. FIG. 12-2 shows the results for antibodies to which a masking molecule (γ) has been attached using a cancer tissue-specific protease-cleavable linker (β). The masking molecule (γ) of the respective antibodies is composed of a sequence of seven amino acids (since the linker portion includes a GG sequence, the sequence up to the ninth amino acid is the same sequence as the CD3ε N-terminus), 20 amino acids, or 27 amino acids from the N-terminus of CD3ε. In both FIGS. 12-1 and 12-2, the solid lines indicate protease-treated antibodies and the dashed lines indicate antibodies not subjected to protease treatment.

FIGS. 13-1 and 13-2 show the results of evaluating CD3ε activation by anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease treatment. The derivatives have been prepared based on an antibody in which the heavy chain is rCE115H and the light chain is GLS3000. FIG. 13-1 shows the results for an unmodified antibody to which no peptide has been attached and an antibody to which a masking molecule (γ) has been attached using a noncleavable GS linker. FIG. 13-2 shows the results for antibodies to which a masking molecule (γ) has been attached using a cancer tissue-specific protease-cleavable linker (β). The masking molecule (γ) of the respective antibodies is composed of a sequence of seven amino acids (since the linker portion includes a GG sequence, the sequence up to the ninth amino acid is the same sequence as the CD3ε N-terminus), 20 amino acids, or 27 amino acids from the N-terminus of CD3ε. In both FIG. 13-1 and FIG. 13-2, the solid lines indicate protease-treated antibodies and the dashed lines indicate antibodies not subjected to protease treatment.

FIGS. 14-1 and 14-2 show the results of evaluating CD3ε activation by anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease treatment. The derivatives have been prepared based on an antibody in which the heavy chain is rCE115H and the light chain is rCE115L. FIG. 14-1 shows the results for an unmodified antibody to which no peptide has been attached and an antibody to which a masking molecule (γ) has been attached using a noncleavable GS linker. FIG. 14-2 shows the results for antibodies to which a masking molecule (γ) has been added using a cancer tissue-specific protease-cleavable linker (β). The masking molecule (γ) of the respective antibodies is composed of a sequence of seven amino acids (since the linker portion includes a GG sequence, the sequence up to the ninth amino acid is the same sequence as the CD3ε N-terminus), 20 amino acids, or 27 amino acids from the N-terminus of CD3ε. In both FIGS. 14-1 and 14-2, the solid lines indicate protease-treated antibodies and the dashed lines indicate antibodies not subjected to protease treatment.

FIGS. 15-1 and 15-2 show the results of evaluating CD3ε activation by anti-CD3 antibody derivatives and non-cleavable antibodies with masked binding to CD3ε after protease treatment. The derivatives have been prepared based on an antibody in which the heavy chain is hCE115HA and the light chain is GLS3000. FIG. 15-1 shows the results for an unmodified antibody to which no peptide has been attached and an antibody to which a masking molecule (γ) has been added using a noncleavable GS linker. FIG. 15-2 shows the results for antibodies to which a masking molecule (γ) has been attached using a cancer tissue-specific protease-cleavable linker (β). The masking molecule (γ) of the respective antibodies is composed of a sequence of seven amino acids (since the linker portion includes a GG sequence, the sequence up to the ninth amino acid is the same sequence as the CD3ε N-terminus), 20 amino acids, or 27 amino acids from the N-terminus of CD3ε. In both FIGS. 15-1 and 15-2, the solid lines indicate protease-treated antibodies and the dashed lines indicate antibodies not subjected to protease treatment.

MODE FOR CARRYING OUT THE INVENTION

Herein, “recognize” means that an antigen-binding region, an antigen-binding molecule, an antibody, an antibody fragment, or such binds to an antigen. “Specifically recognize” means that an antigen-binding region, an antigen-binding molecule, an antibody, an antibody fragment, or such recognizes and binds to a specific three-dimensional structure in an antigen.

Furthermore, “antigen-binding region” indicates a region that is present in a molecule and can recognize an antigen. An antigen-binding region may be formed by a polypeptide or a low-molecular-weight compound excluding polypeptides. An “immune cell antigen-binding region” can recognize an antigen specifically expressed by immune cells, and a “cancer antigen-binding region” can recognize a cancer antigen.

“Masking effect” indicates the effect of preventing an antigen-binding region from binding to its target antigen through binding of a masking molecule to the antigen-binding region.

“Linear peptide” indicates a polypeptide that does not form higher-order structures, or a polypeptide that, when forming higher-order structures, forms secondary structures such as α-helical structures, β-sheet structures, loops, and turns but does not form tertiary structures and quaternary structures. “Linear epitope” indicates a partial linear peptide in an antigen, which is recognized by an antigen-binding region.

Herein, “heavy chain” may be referred to as “H chain”, and “light chain” may be referred to as “L chain”.

The three-letter codes and corresponding one-letter codes of amino acids used herein are defined as follows: alanine: Ala and A, arginine: Arg and R, asparagine: Asn and N, aspartic acid: Asp and D, cysteine: Cys and C, glutamine: Gln and Q, glutamic acid: Glu and E, glycine: Gly and G, histidine: His and H, isoleucine: Ile and I, leucine: Leu and L, lysine: Lys and K, methionine: Met and M, phenylalanine: Phe and F, proline: Pro and P, serine: Ser and S, threonine: Thr and T, tryptophan: Trp and W, tyrosine: Tyr and Y, and valine: Val and V.

A. Multiple Antigen-Binding Molecule Fusion Molecules

Multiple antigen-binding molecule fusion molecules of the present invention comprise a multiple antigen-binding molecule (α), a cancer tissue-specific protease-cleavable linker (β), and a masking molecule (γ).

In such multiple antigen-binding molecule fusion molecules, a multiple antigen-binding molecule (α) and a masking molecule (γ) are linked via a cancer tissue-specific protease-cleavable linker (β).

The type of bond between a multiple antigen-binding molecule (α) and a cancer tissue-specific protease-cleavable linker (β), and the type of bond between a cancer tissue-specific protease-cleavable linker (β) and a masking molecule (γ) are not particularly limited. A preferred type of bond is a peptide bond.

Each component of multiple antigen-binding molecule fusion molecules of the present invention is described in detail below.

Multiple Antigen-Binding Molecule (α)

Multiple antigen-binding molecules (α) of the present invention contain immune cell antigen-binding regions and cancer antigen-binding regions. More specifically, a multiple antigen-binding molecule (α) is a molecule containing an immune cell antigen-binding region and a cancer antigen-binding region within the same molecule, and is not particularly limited as long as it has at least one immune cell antigen-binding region and one cancer antigen-binding region within the same molecule.

An embodiment of the multiple antigen-binding molecules (α) is, for example, a molecule containing a single immune cell antigen-binding region and a single cancer antigen-binding region within the same molecule. A specific example is a bispecific antibody.

Another embodiment of the multiple antigen-binding molecules (α) includes, for example, a molecule made by using techniques such as DART (WO2012/162067), Dual-Fab (PCT/JP2014/079785), 2+1 IgG Crossfab (WO2013/026833), and BiTE (Spiess C et al., Mol. Immunol. (2015) 67 (2) 95-106).

An immune cell antigen-binding region and a cancer antigen-binding region may be linked directly, or they may be linked via a biocompatible linker. However, when an immune cell antigen-binding region is linked to a cancer antigen-binding region via a linker, to enable sufficient induction of cytotoxic activity, the linker is preferably not a cancer tissue-specific protease-cleavable linker (β) described below.

Regarding Immune Cell Antigen-Binding Regions

An immune cell antigen-binding region recognizes an antigen comprising a polypeptide consisting of the amino acid sequence QDGNE (SEQ ID NO: 15). The phrase “recognize an antigen comprising a polypeptide consisting of the amino acid sequence QDGNE (SEQ ID NO: 15)” means that the binding activity to an antigen is decreased or lost when the amino acid sequence QDGNE is deleted.

A decrease in the binding activity can be confirmed by well-known methods such as FACS, ELISA format, screening by Amplified Luminescent Proximity Homogeneous Assay (ALPHA), and BIACORE method which uses the surface plasmon resonance (SPR) phenomenon. The decrease indicates, when the amino acid sequence QDGNE (SEQ ID NO: 15) is deleted from the antigen comprising a polypeptide consisting of the amino acid sequence QDGNE, the binding activity of 50% or less, preferably 45% or less, 40% or less, 35% or less, 30% or less, 20% or less, 15% or less, or particularly preferably 10% or less, 9% or less, 8% or less, 7% or less, 6% or less, 5% or less, 4% or less, 3% or less, 2% or less, or 1% or less as compared to the binding activity to the antigen before the deletion.

Here, the amino acid sequence QDGNE is an amino acid sequence present in the extracellular region of human CD3ε, and is shared between human and cynomolgus monkey (see the arrow in FIG. 1).

An antigen comprising a polypeptide having the amino acid sequence QDGNE is preferably entirely a partial polypeptide of human CD3ε. Furthermore, human CD3ε partial polypeptides are preferably human CD3ε partial polypeptides comprising the amino acid sequence QDGNE at its N terminus. The human CD3εpartial polypeptides having the amino acid sequence QDGNE at its N terminus are preferably a region highly homologous to a corresponding partial polypeptide of cynomolgus CD3ε. The homology is preferably 90% or greater, more preferably 95% or greater, and most preferably 100%. If the homology is high, when a multiple antigen-binding molecule fusion molecule subjected to non-clinical toxicity assays using cynomolgus monkeys is used as it is in clinical trials, the assay results obtained from the non-clinical toxicity assays using cynomolgus monkeys will be likely to reflect the clinical trials.

An antigen comprising a polypeptide having the amino acid sequence QDGNE (SEQ ID NO: 15) may be chemically modified. The chemical modifications may be known modifications. Examples of the chemical modifications include acetylation, alkylation, and pyroglutamylation. Among the modifications, pyroglutamylation of Q in the amino acid sequence QDGNE is preferred.

An immune cell antigen-binding region which recognizes an antigen comprising a polypeptide having the amino acid sequence QDGNE is obtained, for example, by a method that uses a known antibody preparation method.

An antibody obtained by such a preparation method may be used as it is for the immune cell antigen-binding region, or only an Fv region in the obtained antibody may be used. When such an Fv region in the form of a single chain (also referred to as “sc”) can recognize the antigen, the single chain alone may be used. Alternatively, a Fab region containing the Fv region may be used.

Specific methods for preparing antibodies are well known to those skilled in the art. For example, monoclonal antibodies may be produced by a hybridoma method (Kohler and Milstein, Nature 256: 495 (1975)) or a recombination method (U.S. Pat. No. 4,816,567). Alternatively, monoclonal antibodies may be isolated from phage-displayed antibody libraries (Clackson et al., Nature 352: 624-628 (1991); and Marks et al., J. Mol. Biol. 222: 581-597 (1991)). Also, monoclonal antibodies may be isolated from single B cell clones (N. Biotechnol. 28 (5): 253-457 (2011)).

A humanized antibody is also called a reshaped human antibody. Specifically, humanized antibodies prepared by grafting the CDR of a non-human animal antibody such as a mouse antibody to a human antibody and such are known. Common genetic engineering techniques for obtaining humanized antibodies are also known. Specifically, for example, overlap extension PCR is known as a method for grafting a mouse antibody CDR to a human FR.

DNAs encoding antibody variable regions comprising three CDRs and four FRs linked and DNAs encoding human antibody constant regions can be inserted into expression vectors such that the variable region DNAs are fused in frame with the constant region DNAs to prepare vectors for humanized antibody expression. These vectors having the inserts are transferred to hosts to establish recombinant cells. Then, the recombinant cells are cultured for the expression of the DNAs encoding the humanized antibodies to produce the humanized antibodies into the cultures of the cultured cells (see European Patent Application Publication No. EP 239400 and WO 1996/002576).

If necessary, FR amino acid residue(s) may be substituted such that the CDRs of the reshaped human antibody form an appropriate antigen-binding site. For example, the amino acid sequences of FR can be mutated by the application of the PCR method used in the mouse CDR grafting to the human FRs.

The desired human antibody can be obtained by DNA immunization using transgenic animals having all repertoires of human antibody genes (see WO1993/012227, WO 1992/003918, WO 1994/002602, WO 1994/025585, WO 1996/034096, and WO1996/033735) as immunized animals.

In addition, a technique of obtaining human antibodies by panning using human antibody libraries is also known. For example, a human antibody Fv region is expressed as a single-chain antibody (also referred to as “scFv”) on the surface of phages by a phage display method. A phage expressing antigen-binding scFv can be selected. The gene of the selected phage can be analyzed to determine a DNA sequence encoding the Fv region of the antigen-binding human antibody. After determination of the DNA sequence of the antigen-binding scFv, the Fv region sequence can be fused in frame with the sequence of the desired human antibody C region and then inserted to appropriate expression vectors to prepare expression vectors. The expression vectors are introduced into preferred expression cells listed above for the expression of the genes encoding the human antibodies to obtain the human antibodies. These methods are already known in the art (see WO1992/001047, WO1992/020791, WO1993/006213, WO1993/011236, WO1993/019172, WO1995/001438, and WO1995/015388).

The binding activity of an immune cell antigen-binding region to an immune cell antigen can be enhanced by panning. The binding activity of an immune cell antigen-binding region to an immune cell antigen is calculated from data from binding assays that use the surface plasmon resonance (SPR) method (for example, using Biacore T200) or such. Binding activity is indicated by KD (M), and a smaller KD (M) indicates a higher binding activity. The KD (M) is preferably smaller than 10⁻⁶, and more preferably smaller than 10⁻⁷.

For an immune cell antigen-binding region which recognizes an antigen comprising a polypeptide consisting of the amino acid sequence QDGNE, an antibody or antibody fragment newly obtained by an antibody preparation method as described above may be used, or a known antibody or antibody fragment that can recognize the antigen may be used. Examples of the known antibody or antibody fragment that can recognize an antigen comprising a polypeptide having the amino acid sequence QDGNE include scFvs prepared in the Examples of WO2007/042261 and WO2002008/119567.

In addition to such scFvs, examples include CE115 disclosed in PCT/JP2014/079785. The method for preparing CE115 will be described later in Reference Example 1.

The immune cell antigen-binding regions of the present invention may only recognize antigens comprising a polypeptide having the amino acid sequence QDGNE, or may recognize antigens comprising a polypeptide consisting of the amino acid sequence QDGNE as well as at least one type of immune cell antigen other than such antigens.

The immune cell antigen-binding regions of the present invention are preferably those that recognize antigens comprising a polypeptide having the amino acid sequence QDGNE as well as at least one type of immune cell antigen other than such antigens.

Examples of immune cell antigens other than the antigen comprising a polypeptide having the amino acid sequence QDGNE include T cell surface molecules, NK cell surface molecules, dendritic cell surface molecules, B cell surface molecules, NKT cell surface molecules, MDSC cell surface molecules, and macrophage surface molecules.

Specific examples of T cell surface molecules include CD3 and T cell receptors. However, in the case of CD3, it is a molecule which does not comprise a polypeptide having the amino acid sequence QDGNE. As long as the T cell surface molecules do not comprise a polypeptide having the amino acid sequence QDGNE, for example, in the case of human CD3, they may be those that bind to any epitope as long as the epitope is present in the γ chain, δ chain, or ε chain sequences that constitute human CD3.

Specific examples of immune cell antigens other than T cell surface molecules include Fcγ receptors, TLR, lectins, IgA, immune checkpoint molecules, TNF superfamily molecules, TNF receptor superfamily molecules, and NK receptor molecules.

In particular, in terms of further improvement of the cytotoxic activity against cancer cells by recruiting, in addition to T cells, various immune cells other than T cells such as NK cells to cancer cells, immune cell antigens to be recognized, other than antigens comprising a polypeptide having the amino acid sequence QDGNE, are preferably at least those selected from the group consisting of NK cell surface molecules, dendritic cell surface molecules, B cell surface molecules, NKT cell surface molecules, MDSC cell surface molecules, and macrophage surface molecules.

When an immune cell antigen-binding region is made to recognize an antigen comprising a polypeptide having the amino acid sequence QDGNE and additionally at least one type of immune cell antigen other than said antigen, it is preferable that the immune cell antigen-binding region does not recognize two or more immune cell antigens simultaneously. By preparing an immune cell antigen-binding region so that it cannot recognize two or more immune cell antigens simultaneously, the multiple antigen-binding molecule fusion molecule becomes a molecule that cannot recognize multiple immune cells simultaneously. If a multiple antigen-binding molecule fusion molecule can recognize several immune cells simultaneously, these several immune cells may interfere with each other and consequently induce abnormal immune responses, and increase the occurrence of side effects. Therefore, by preparing the immune cell antigen-binding region so that it cannot recognize two or more immune cell antigens simultaneously, the possibility of side effects can be decreased.

Techniques of making an immune cell antigen-binding region recognize an antigen comprising a polypeptide having the amino acid sequence QDGNE and additionally at least one type of immune cell antigen other than said antigen, and making the immune cell antigen-binding region not able to recognize two or more immune cell antigens simultaneously include, for example, the Dual-Fab technology. The Dual-Fab technology is a technology that enables a single Fab to recognize two or more antigens, and is disclosed in PCT/JP2014/079785. A specific example of a method for producing antigen-binding molecules by the Dual-Fab technology is a production method comprising the following steps (i) to (iv):

-   (i) preparing a library of antigen-binding molecules with at least     one amino acid altered in their antibody variable regions each     binding to a first antigen or a second antigen, wherein the altered     variable regions differ in at least one amino acid from each other; -   (ii) selecting, from the prepared library, an antigen-binding     molecule containing a variable region that has binding activity     against the first antigen and the second antigen, but does not bind     to the first antigen and the second antigen at the same time; -   (iii) culturing a host cell comprising a nucleic acid encoding the     variable region of the antigen-binding molecule selected in the step     (ii), to express an immune cell antigen-binding region containing     the antibody variable region that can bind to the first antigen and     the second antigen but does not bind to the first antigen and the     second antigen at the same time; and -   (iv) recovering the antigen-binding molecule from the host cell     culture.     In this production method, the step (ii) may be the following step     (v): -   (v) selecting, from the prepared library, an antigen-binding     molecule containing a variable region that has binding activity     against the first antigen and the second antigen, but does not bind     to the first antigen and the second antigen each expressed on a     different cell, at the same time.

Regarding Cancer Antigen-Binding Regions

Cancer antigen-binding regions recognize cancer antigens. A function of such regions is, for example, to highly concentrate multiple antigen-binding molecule fusion molecules at cancer tissues by their recognition of cancer antigens.

Cancer antigen-binding regions are not particularly limited so long as they can recognize cancer antigens. More specifically, a cancer antigen-binding region may be a polypeptide such as Fv of an antibody that recognizes a cancer antigen, or it may be a low-molecular-weight compound other than polypeptides, such as folic acid. In the case it is a low-molecular-weight compound, a step of linking the cancer antigen-binding region to an immune cell antigen-binding region becomes necessary for producing a multiple antigen-binding molecule (α). Therefore, the cancer antigen-binding region is preferably a polypeptide, since in that case, a multiple antigen-binding molecule (α) can be produced simply by allowing cells to express it and this will enable an increase in production efficiency.

A cancer antigen is a tumor cell-specific antigen, and includes an antigen expressed in association with the malignant alteration of cells, and also an abnormal sugar chain that appears on the cell surface or on a protein molecule during the malignant transformation of cells.

Specific examples of a cancer antigen include glypican-3 (GPC3), ALK receptor (pleiotrophin receptor), pleiotrophin, KS 1/4 pancreatic cancer antigen, ovary cancer antigen (CA125), prostatic acid phosphate, prostate-specific antigen (PSA), melanoma-associated antigen p97, melanoma antigen gp75, high-molecular-weight melanoma antigen (HMW-MAA), prostate-specific membrane antigen, carcinoembryonic antigen (CEA), polymorphic epithelial mucin antigen, human milk fat globule antigen, colorectal tumor-associated antigen (e.g., CEA, TAG-72, CO17-1A, GICA 19-9, CTA-1, and LEA), Burkitt's lymphoma antigen 38.13, CD19, human B lymphoma antigen CD20, CD33, melanoma-specific antigen (e.g., ganglioside GD2, ganglioside GD3, ganglioside GM2, and ganglioside GM3), tumor-specific transplantation antigen (TSTA), T antigen, virus-induced tumor antigen (e.g., envelope antigens of DNA tumor virus and RNA tumor virus), colon CEA, oncofetal antigen α-fetoprotein (e.g., oncofetal trophoblastic glycoprotein 5T4 and oncofetal bladder tumor antigen), differentiation antigen (e.g., human lung cancer antigens L6 and L20), fibrosarcoma antigen, human T cell leukemia-associated antigen Gp37, newborn glycoprotein, sphingolipid, breast cancer antigen (e.g., EGFR (epithelial growth factor receptor)), NY-BR-16, NY-BR-16 and HER2 antigen (p185HER2), polymorphic epithelial mucin (PEM), malignant human lymphocyte antigen APO-1, differentiation antigen such as I antigen found in fetal erythrocytes, primary endoderm I antigen found in adult erythrocytes, I (Ma) found in embryos before transplantation or gastric cancer, M18 found in mammary gland epithelium, M39, SSEA-1 found in bone marrow cells, VEP8, VEP9, Myl, VIM-D5, D156-22 found in colorectal cancer, TRA-1-85 (blood group H), SCP-1 found in testis and ovary cancers, C14 found in colon cancer, F3 found in lung cancer, AH6 found in gastric cancer, Y hapten, Ley found in embryonic cancer cells, TL5 (blood group A), EGFR found in A431 cells, E1 series (blood group B) found in pancreatic cancer, FC10.2 found in embryonic cancer cells, gastric cancer antigen, CO-514 (blood group Lea) found in adenocarcinoma, NS-10 found in adenocarcinoma, CO-43 (blood group Leb), G49 found in A431 cell EGFR, MH2 (blood group ALeb/Ley) found in colon cancer, 19.9 found in colon cancer, gastric cancer mucin, T5A7 found in bone marrow cells, R24 found in melanoma, 4.2, GD3, D1.1, OFA-1, GM2, OFA-2, GD2, and M1:22:25:8 found in embryonic cancer cells, SSEA-3 and SSEA-4 found in 4-cell to 8-cell embryos, cutaneous T cell lymphoma-associated antigen, MART-1 antigen, sialyl Tn (STn) antigen, colon cancer antigen NY-CO-45, lung cancer antigen NY-LU-12 variant A, adenocarcinoma antigen ART1, paraneoplastic associated brain-testis-cancer antigen (onconeuronal antigen MA2 and paraneoplastic neuronal antigen), neuro-oncological ventral antigen 2 (NOVA2), blood cell cancer antigen gene 520, tumor-associated antigen CO-029, tumor-associated antigen MAGE-C1 (cancer/testis antigen CT7), MAGE-B1 (MAGE-XP antigen), MAGE-B2 (DAM6), MAGE-2, MAGE-4a, MAGE-4b MAGE-X2, cancer-testis antigen (NY-EOS-1), YKL-40, and any fragment of these polypeptides, and modified structures thereof (aforementioned modified phosphate groups, sugar chains, etc.), EpCAM, EREG, CA19-9, CA15-3, sialyl SSEA-1 (SLX), HER2, PSMA, CEA, and CLEC12A. Among the above, GPC3, EGFR, and p185HER2 are preferred, and GPC3 is more preferred.

Furthermore, beside antigens directly expressed by cancer cells such as those presented as examples above, cancer antigens may be antigens that are not expressed by cancer cells but exist inside or near cancer tissues and promote proliferation and metastases of cancer cells.

Cancer antigen-binding regions are obtained, for example, by a method that uses a known antibody preparation method.

An antibody obtained by such a preparation method may be used as it is for the cancer antigen-binding region, or only an Fv region in the obtained antibody may be used. When such an Fv region in the form of a single chain can recognize the antigen, the single chain alone may be used. Alternatively, a Fab region containing the Fv region may be used.

A specific antibody preparation method may be carried out in a similar manner to the specific antibody preparation method for the above-described immune cell antigen-binding region.

Furthermore, similarly to the binding activity of an immune cell antigen-binding region to an immune cell antigen, the binding activity of a cancer antigen-binding region to a cancer antigen can be enhanced by panning. The binding activity of an immune cell antigen-binding region to an immune cell antigen is calculated from data from binding assays that use the surface plasmon resonance (SPR) method (for example, using Biacore T200). Binding activity is indicated by KD (M), and a smaller KD (M) indicates a higher binding activity. The KD (M) is preferably smaller than 10⁻⁶, more preferably smaller than 10⁻⁷, and even more preferably smaller than 10⁻⁸.

An Embodiment of Multiple Antigen-Binding Molecules (α)

Examples of an embodiment of multiple antigen-binding molecules (α) include antibodies and antibody fragments, and their fusion molecules and complexes, and such.

Herein, “antibody” is used in the broadest sense and also includes any antibody such as monoclonal antibodies (including full-length monoclonal antibodies), polyclonal antibodies, antibody variants, antibody fragments, multispecific antibodies (e.g., bispecific antibodies), chimeric antibodies, and humanized antibodies as long as the antibody exhibits the desired biological activity.

Moreover, the antibody is not limited by the type of its antigen, its origin, or such, and may be any antibody. Examples of the origin of the antibody can include, but are not particularly limited to, human antibodies, mouse antibodies, rat antibodies, and rabbit antibodies.

Among those described above, an example of a preferred antibody is a multispecific antibody. A multispecific antibody is an antibody that can recognize two or more antigens. When a multispecific antibody is used as the multiple antigen-binding molecule (α), the cancer antigen-binding region and the immune cell antigen-binding region are preferably formed by different Fv regions.

Multispecific antibodies can be produced by known production methods. Specifically, the following methods are given as examples.

An amino acid side chain present in the variable region of one antibody H chain is substituted by a larger side chain (knob), and its partner amino acid side chain present in the variable region of the other H chain is substituted by a smaller side chain (hole). The knob can be placed into the hole to efficiently associate polypeptides of the Fc regions differing in amino acid sequence (WO1996/027011; Ridgway J B et al., Protein Engineering (1996) 9, 617-621; and Merchant A M et al. Nature Biotechnology (1998) 16, 677-681).

The association of polypeptides having different sequences can be efficiently triggered by complementary association of CH3 using strand-exchange engineered domain CH3, in which a portion of CH3 of one H chain of an antibody is changed to a sequence derived from IgA corresponding to that portion, and a complementary portion of CH3 of the other H chain is introduced with a sequence derived from IgA corresponding to that portion (Protein Engineering Design & Selection, 23: 195-202, 2010).

Alternatively usable techniques are, for example, an antibody preparation technique using antibody CH1-CL association and H chain variable region (hereinafter abbreviated as “VH”)-L chain variable region (hereinafter abbreviated as “VL”) association as described in WO2011/028952, WO2014/018572, and Nat. Biotechnol. 2014 February; 32(2):191-8, a technique of preparing a bispecific antibody using separately prepared monoclonal antibodies (Fab Arm Exchange (also abbreviated as “FAE”)) as described in WO2008/119353 and WO2011/131746, a technique of controlling the association between antibody heavy chain CH3 as described in WO2012/058768 and WO2013/063702, a technique of preparing a bispecific antibody constituted by two types of light chains and one type of heavy chain as described in WO2012/023053, or a technique of preparing a bispecific antibody using two bacterial cell lines each expressing an antibody half-molecule consisting of one H chain and one L chain as described in Christoph et al. (Nature Biotechnology Vol. 31, p. 753-758 (2013)).

Further, the CrossMab technique, a known hetero light chain association technique of associating a light chain forming a variable region binding to a first epitope and a light chain forming a variable region binding to a second epitope to a heavy chain forming a variable region binding to the first epitope and a heavy chain forming a variable region binding to the second epitope, respectively (Scaefer et al., Proc. Natl. Acad. Sci. U.S.A. (2011) 108, 11187-11192), can also be used for preparing a multispecific antibody.

Among these methods for producing multispecific antibodies, FAE is preferred. Examples of FAE include the methods described in WO2006/106905 and WO2015/046467, in which undesired association between H chains is suppressed by introducing electric charge repulsion at the interface of the second constant region of the antibody H chain (CH2) or the third constant region of the antibody H chain (CH3). In FAE which uses naturally-occurring IgG, re-association occurs randomly, and therefore bispecific antibodies can only be obtained at a theoretical efficiency of 50%; however, by the above-mentioned method, bispecific antibodies can be produced in high yield. This method is described in detail below.

In the technique of suppressing the unintended association between H chains by introducing electric charge repulsion to the CH2 or CH3 interface, examples of amino acid residues contacting with each other at the interface between the H chain constant regions can include a residue at EU numbering position 356, a residue at EU numbering position 439, a residue at EU numbering position 357, a residue at EU numbering position 370, a residue at EU numbering position 399, and a residue at EU numbering position 409 in one CH3 region, and their partner residues in another CH3 region.

More specifically, for example, in an antibody containing two types of H chain CH3 regions, one to three pairs of amino acid residues selected from the following amino acid residue pairs (1) to (3) in the first H chain CH3 region may be made to carry the same electric charge:

-   -   (1) the amino acid residues contained in the H chain CH3 region         at position 356 and position 439 as indicated by EU numbering;     -   (2) the amino acid residues contained in the H chain CH3 region         at position 357 and position 370 as indicated by EU numbering;         and     -   (3) the amino acid residues contained in the H chain CH3 region         at position 399 and position 409 as indicated by EU numbering.

Moreover, the antibody can be an antibody in which one to three pairs of amino acid residues in the second H chain CH3 region different from the above first H chain CH3 region are selected from the amino acid residue pairs shown in (1) to (3) above, correspond to the amino acid residue pairs shown in (1) to (3) above carrying the same electric charge in the first H chain CH3 region, and have opposite electric charge from the corresponding amino acid residues in the first H chain CH3 region.

The amino acid residues described in (1) to (3) above approach each other upon association. Those skilled in the art would be able to find positions corresponding to the amino acid residues described in (1) to (3) mentioned above for a desired H chain CH3 region or H chain constant region by homology modeling and such using commercially available software, and to suitably modify the amino acid residues at those positions.

In the antibody described above, each of the “amino acid residues carrying electric charge” is preferably selected from, for example, amino acid residues included in any of the following groups (a) and (b):

-   -   (a) glutamic acid (E) and aspartic acid (D); and     -   (b) lysine (K), arginine (R), and histidine (H).

In the antibody described above, the phrase “carrying the same electric charge” means that, for example, any two or more amino acid residues have amino acid residues that are contained in either one group of (a) and (b) mentioned above. “Having an opposite charge” means that, for example, when at least one amino acid residue among two or more amino acid residues is an amino acid residue contained in either one group of (a) and (b) mentioned above, the other amino acid residue(s) is an amino acid residue(s) contained in a different group.

In a preferred embodiment of the antibody as described above, the first H chain CH3 region and the second H chain CH3 region may be cross-linked by disulfide bonds.

An amino acid residue subjected to modification is not limited to an amino acid residue of the antibody variable region or antibody constant region mentioned above. Those skilled in the art would be able to find amino acid residues that form an interface in a polypeptide variant or heteromeric multimer by homology modeling and the like using commercially available software, and to modify amino acid residues at those sites so as to regulate association.

A plurality of, for example, two or more of these techniques for producing multispecific antibodies may be used in combination. Also, these techniques can be appropriately applied separately to the two H chains to be associated.

If a multispecific antibody cannot be formed efficiently, a multispecific antibody of interest can also be separated and purified from produced multispecific antibodies. For example, the previously reported method involves introducing amino acid substitutions to the variable regions of two types of H chains to impart thereto a difference in isoelectric points so that two types of homodimers and a heterodimerized antibody of interest can be purified by ion-exchanged chromatography (WO2007/114325). A method using protein A to purify a heterodimerized antibody consisting of a mouse IgG2a H chain that binds to protein A and a rat IgG2b H chain that does not bind to protein A has previously been reported as a method for purifying heterodimers (WO98/050431 and WO95/033844). Further, H chains in which amino acid residues at EU numbering positions 435 and 436 that constitute the protein A-binding site of IgG may be substituted with amino acids, such as Tyr and His, which offer the different binding force toward protein A, is used to change the interaction of each H chain with protein A, and only heterodimerized antibodies can be efficiently purified by using a protein A column.

Antibody fragments, when used as the multispecific antigen binding molecule (α) of the present embodiment, include those that contain both of a heavy chain and a light chain in a single polypeptide chain but lack a constant region. Specific examples of such antibody fragments include diabodies (Db), single-chain antibodies, and sc(Fab′)2.

A Db is a dimer constituted by two polypeptide chains (e.g., Holliger P et al., Proc. Natl. Acad. Sci. USA 90: 6444-6448 (1993); EP404,097; and WO93/11161). The polypeptide chains are linked through a linker as short as, for example approximately 5 residues, such that a VL and a VH on the same polypeptide chain cannot be paired with each other.

Because of this short linker, VL and VH encoded on the same polypeptide chain cannot form a single-chain variable region fragment and form two antigen binding sites by dimerization.

Examples of the single-chain antibody include sc(Fv)2. An sc(Fv)2 is a single-chain antibody having one chain constituted by four variable regions, i.e., two VLs and two VHs, linked via linkers such as peptide linkers (J Immunol. Methods (1999) 231 (1-2), 177-189). These two VHs and VLs may be derived from different monoclonal antibodies. Preferred examples thereof include bispecific sc(Fv)2, which recognizes two types of epitopes present in the same antigen, as disclosed in Journal of Immunology (1994) 152 (11), 5368-5374. The sc(Fv)2 may be prepared by a method known to those skilled in the art. For example, the sc(Fv)2 can be prepared by connecting two scFvs via a linker such as a peptide linker.

Examples of the configuration of the antigen-binding domains constituting an sc(Fv)2 include an antibody in which two VHs and two VLs are aligned as VH, VL, VH, and VL (i.e., [VH]-linker-[VL]-linker-[VH]-linker-[VL]) in this order starting from the N-terminus of the single-chain polypeptide. The order of two VHs and two VLs is not particularly limited to the configuration described above and may be any order of arrangement. Examples include the following arrangements:

[VL]-linker-[VH]-linker-[VH]-linker-[VL],

[VH]-linker-[VL]-linker-[VL]-linker-[VH],

[VH]-linker-[VH]-linker-[VL]-linker-[VL],

[VL]-linker-[VL]-linker-[VH]-linker-[VH], and

[VL]-linker-[VH]-linker-[VL]-linker-[VH].

The molecular form of the sc(Fv)2 is also described in detail in WO2006/132352. On the basis of the description therein, those skilled in the art can appropriately prepare a desired sc(Fv)2 in order to prepare the multispecific antigen binding molecule (α) of the present embodiment.

An arbitrary peptide linker that can be introduced by genetic engineering or a synthetic compound linker (e.g., a linker disclosed in Protein Engineering, 9 (3), 299-305, 1996) can be used as the linker to link the variable regions. In the present embodiment, a peptide linker is preferred. The length of the peptide linker is not particularly limited and can be appropriately selected by those skilled in the art according to the purpose. The length is preferably 5 amino acids or more (the upper limit is not particularly limited and is usually 30 amino acids or less, preferably 20 amino acids or less), and particularly preferably 15 amino acids. When the sc(Fv)2 contains three peptide linkers, all of these peptide linkers used may have the same lengths or may have different lengths.

Examples of the peptide linker can include:

Ser, Gly-Ser, Gly-Gly-Ser, Ser-Gly-Gly, Gly-Gly-Gly-Ser (SEQ ID NO: 1), Ser-Gly-Gly-Gly (SEQ ID NO: 2), Gly-Gly-Gly-Gly-Ser (SEQ ID NO: 3), Ser-Gly-Gly-Gly-Gly (SEQ ID NO: 4), Gly-Gly-Gly-Gly-Gly-Ser (SEQ ID NO: 5), Ser-Gly-Gly-Gly-Gly-Gly (SEQ ID NO: 6), Gly-Gly-Gly-Gly-Gly-Gly-Ser (SEQ ID NO: 7), Ser-Gly-Gly-Gly-Gly-Gly-Gly (SEQ ID NO: 8), (Gly-Gly-Gly-Gly-Ser (SEQ ID NO: 3))n, and (Ser-Gly-Gly-Gly-Gly (SEQ ID NO: 4))n, wherein n is an integer of 1 or larger. However, the length and sequence of the peptide linker can be appropriately selected by those skilled in the art according to the purpose.

A synthetic compound linker (chemical cross-linking agent) is a cross-linking agent usually used in the cross-linking of peptides, for example, N-hydroxysuccinimide (NHS), disuccinimidyl suberate (DSS), bis(sulfosuccinimidyl) suberate (BS3), dithiobis(succinimidyl propionate) (DSP), dithiobis(sulfosuccinimidyl propionate) (DTSSP), ethylene glycol bis(succinimidyl succinate) (EGS), ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS), disuccinimidyl tartrate (DST), disulfosuccinimidyl tartrate (sulfo-DST), bis[2-(succinimidoxycarbonyloxy)ethyl]sulfone (BSOCOES), or bis[2-(sulfosuccinimidoxycarbonyloxy)ethyl]sulfone (sulfo-BSOCOES).

These cross-linking agents are commercially available.

Three linkers are usually necessary for linking four antibody variable regions. All of these linkers used may be the same linkers or may be different linkers.

An F(ab′)2 comprises two light chains and two heavy chains containing a constant region composed of a CH1 domain and a portion of the CH2 domain so as to form the interchain disulfide bonds between these two heavy chains. The F(ab′)2 constituting a multispecific antigen binding molecule (α) can be suitably obtained by the partial digestion of, for example, a full-length monoclonal antibody having the desired antigen-binding domains with a proteolytic enzyme such as pepsin, followed by the removal of Fc fragments by adsorption on a protein A column. Such a proteolytic enzyme is not particularly limited as long as it is capable of digesting full-length antibodies to restrictively form F(ab′)₂ by appropriately setting the enzymatic reaction conditions such as the pH. Examples thereof include pepsin and ficin.

From the viewpoint of obtaining superior cytotoxicity, antibody fragments preferably comprise at least two Fv fragments, and the cancer antigen-binding region and the immune cell antigen-binding region are preferably formed by different Fv regions.

Antibody fragments may or may not comprise an Fc region.

An Fc region may be, for example, an Fc region derived from a naturally occurring IgG or may be an Fc region prepared by artificial introduction of mutations into an Fc region derived from a naturally occurring IgG.

In this context, a naturally occurring IgG means a polypeptide that contains an amino acid sequence identical to that of IgG found in nature and belongs to the class of antibodies substantially encoded by an immunoglobulin gamma gene. A naturally occurring human IgG means, for example, a naturally occurring human IgG1, a naturally occurring human IgG2, a naturally occurring human IgG3, or a naturally occurring human IgG4. A naturally occurring IgG also includes variants or the like that are spontaneously derived therefrom. Examples of the variants include, for example, a plurality of allotype sequences based on gene polymorphism (Sequences of proteins of immunological interest, NIH Publication No. 91-3242). In particular, the sequence of human IgG1 may have DEL or EEM as an amino acid sequence at EU numbering positions 356 to 358.

A multiple antigen-binding molecule (α) preferably does not have an Fc region from the viewpoint of preventing occurrence of side effects due to abnormalities such as overly enhanced activity of immune cells caused by an interference between immune cells recruited by an immune cell antigen-binding region and immune cells recruited by an Fc region. However, even if it has an Fc region, the above-mentioned side effects can be reduced if the Fc region is modified so as to lack the function of recognizing Fcγ receptors.

Amino acid sequences can be modified according to various methods known in the art. Examples of these methods include, but are not limited to, site-directed mutagenesis (Hashimoto-Gotoh, T., Mizuno, T., Ogasahara, Y. and Nakagawa, M. (1995) An oligodeoxyribonucleotide-directed dual amber method for site-directed mutagenesis, Gene 152, 271-275; Zoller, M. J. and Smith, M. (1983) Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors, Methods Enzymol. 100, 468-500; Kramer, W., Drutsa, V., Jansen, H. W., Kramer, B., Pflugfelder, M. and Fritz, H. J. (1984) The gapped duplex DNA approach to oligonucleotide-directed mutation construction, Nucleic Acids Res. 12, 9441-9456; Kramer, W. and Fritz, H. J. (1987) Oligonucleotide-directed construction of mutations via gapped duplex DNA, Methods Enzymol. 154, 350-367; Kunkel, T. A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection, Proc. Natl. Acad. Sci. USA 82, 488-492), PCR mutagenesis, cassette mutagenesis, etc.

Whether or not the Fc region is modified so as to lack the function of recognizing an Fcγ receptor can be confirmed by well-known methods such as FACS, ELISA format, ALPHAScreen (Amplified Luminescent Proximity Homogeneous Assay), and the BIACORE method which uses the surface plasmon resonance (SPR) phenomenon (Proc. Natl. Acad. Sci. USA (2006) 103 (11), 4005-4010).

ALPHAScreen is carried out, according to the following principle, based on the ALPHA technology which uses two types of beads (donor and acceptor): molecules bound to the donor beads biologically interact with molecules bound to the acceptor beads, and only when these two beads are located in proximity, a luminescence signal is detected. A laser-excited photosensitizer in the donor beads converts ambient oxygen to singlet oxygen in an excited state. The singlet oxygen diffuses around the donor beads, reaches the acceptor beads located in proximity thereto to thereby cause a chemiluminescent reaction in the beads which finally emit light. In the absence of the interaction between the molecule bound to the donor beads and the molecule bound to the acceptor beads, singlet oxygen produced by the donor beads does not reach the acceptor beads; thus, no chemiluminescent reaction occurs.

For example, a biotin-labeled antigen-binding molecule is allowed to bind to the donor beads, while a glutathione S-transferase (GST)-tagged Fcγ receptor is allowed to bind to the acceptor beads. In the absence of a competing antigen-binding molecule having a mutated Fc region, an antigen-binding molecule having a wild-type Fc region interacts with the Fcγ receptor to generate signals of 520 to 620 nm. The untagged antigen-binding molecule having a mutated Fc region competes with the antigen-binding molecule having a wild-type Fc region for the interaction with the Fcγ receptor. Decrease in fluorescence caused as a result of the competition can be quantified to thereby determine relative binding affinity. Biotinylation of an antigen-binding molecule (e.g., antibody) using sulfo-NHS-biotin or the like is known in the art. An Fcγ receptor can be tagged with GST, by suitably using a method which involves, for example, fusing a polynucleotide encoding the Fcγ receptor in frame with a polynucleotide encoding GST and allowing the resulting fusion gene to be expressed in cells harboring a vector capable of expression thereof or such, followed by purification using a glutathione column. The obtained signals are preferably analyzed using, for example, software GRAPHPAD PRISM (GraphPad Software, Inc., San Diego) adapted to a one-site competition model based on nonlinear regression analysis.

One of the substances between which the interaction is to be observed (ligand) is immobilized onto a thin gold film of a sensor chip. The sensor chip is irradiated with light from the back such that total reflection occurs at the interface between the thin gold film and glass. As a result, a site having a drop in reflection intensity (SPR signal) is formed in a portion of reflected light. The other of the substances between which the interaction is to be observed (analyte) is injected on the surface of the sensor chip. Upon binding of the analyte to the ligand, the mass of the immobilized ligand molecule is increased to change the refractive index of the solvent on the sensor chip surface. This change in the refractive index shifts the position of the SPR signal (on the contrary, bond dissociation gets the signal back to the original position). The Biacore system plots on the ordinate the amount of the shift, i.e., change in mass on the sensor chip surface, and displays time-dependent change in mass as assay data (sensorgram). Kinetics, i.e., the association rate constant (ka) and dissociation rate constant (kd), can be determined from the curve of the sensorgram, while affinity (KD) can be determined from the ratio between these constants. Inhibition assay is also suitably used in the BIACORE method. Examples of the inhibition assay are described in Proc. Natl. Acad. Sci. USA (2006) 103 (11), 4005-4010.

An Fc region lacking the function of recognizing an Fcγ receptor means, for example, an Fc region to be tested having Fcγ receptor-binding activity of 50% or lower, preferably 45% or lower, 40% or lower, 35% or lower, 30% or lower, 20% or lower, or 15% or lower, particularly preferably 10% or lower, 9% or lower, 8% or lower, 7% or lower, 6% or lower, 5% or lower, 4% or lower, 3% or lower, 2% or lower, or 1% or lower as compared with that of a control Fc region based on the analysis method described above.

The control Fc region is, for example, the above-mentioned naturally-occurring IgG-derived Fc region. Furthermore, when an Fc region to be tested is a mutant of an Fc region of a specific isotype antibody, whether or not the mutant lacks the function of recognizing an Fcγ receptor can be examined by using such an Fc region of a specific isotype antibody as the control Fc region.

As such, Fc regions verified to lack the function of recognizing an Fcγ receptor are suitably used as antibody fragments.

Regarding Commonly Shared Light Chains

Preferably, both light chains in an antibody or an antibody fragment having at least two Fv regions have a same amino acid sequence. When both light chains in an antibody or an antibody fragment having at least two Fv regions have a same amino acid sequence, the number of heavy and light chain combinations is decreased; therefore, the step of removing antibodies or antibody fragments having undesired combinations can be facilitated during production. Accordingly, efficiency of production of multiple antigen-binding molecule fusion molecules can be enhanced.

Cancer Tissue-Specific Protease-Cleavable Linker (β)

A cancer tissue-specific protease-cleavable linker (β) comprises a polypeptide containing a sequence targeted by a cancer tissue-specific protease. A cancer tissue-specific protease-cleavable linker (β) may have only a target sequence for a cancer tissue-specific protease, or it may have, in addition to the target sequence, a peptide linker fused thereto. An example of such a peptide linker is a linker that is the same as the above-mentioned linker that links the variable regions.

Cancer tissue-specific protease-cleavable linkers (β) are hydrolyzed by cancer tissue-specific proteases in cancer tissues. When cancer tissue-specific protease-cleavable linkers (β) are hydrolyzed, masking molecules (γ) become dissociable from multiple antigen-binding molecules (α). Upon dissociation of the masking molecules (γ) from the multiple antigen-binding molecules (α), the immune cell antigen-binding regions in the multiple antigen-binding molecules (α) become capable of binding to immune cells.

Furthermore, the cancer tissue-specific protease-cleavable linkers (β) have a function of serving as a spacer so that the masking molecules (γ) can mask the immune cell antigen-binding regions in the multiple antigen-binding molecules (α).

Regarding Target Sequences for Cancer Tissue-Specific Proteases

Examples of cancer tissue-specific proteases include proteases specifically expressed in cancer tissues as disclosed in WO2013/128194, WO2010/081173, WO2009/025846, and such. While not construed as being limited thereto, specific examples of the proteases include cysteine proteases (including the cathepsin family B, L, S, etc.), aspartyl proteases (including cathepsin D, E, K, O, etc.), serine proteases (including cathepsin A and G, thrombin, plasmin, urokinase (uPA), tissue plasminogen activator (tPA)), metalloproteinases (metalloproteinases (MMP1-28) including both membrane-bound form (MMP14-17 and MMP24-25) and secreted form (MMP1-13 and MMP18-23 and MMP26-28), α-disintegrin-and-metalloproteinase (ADAM) proteases, α-disintegrin and metalloproteinase with Thrombospondin motifs (ADAMTS)), CD10 (CALLA), and prostate specific antigens (PSA).

Regarding the types of cancer tissue-specific proteases, as they are expressed in a highly tissue-specific manner in cancer tissues to be treated, a side-effect-decreasing effect provided by the masking molecule (γ) becomes greater. The concentration of a cancer tissue-specific protease in a cancer tissue is higher than in a normal tissue preferably by 5-fold or more, more preferably by 10-fold or more, even more preferably by 100-fold or more, and particularly preferably by 500-fold or more, and most preferably by 1000-fold or more.

Furthermore, cancer tissue-specific proteases may be bound to the cell membrane of cancer cells, or may be unbound to the cell membrane but extracellularly secreted. When cancer tissue-specific proteases are not bound to the cancer cell membrane, cancer tissue-specific proteases are preferably present near or inside cancer tissues in order for immune cells to be specific to cancer cells. Herein, “near cancer tissues” means within a range where cancer cells are damaged by immune cells recruited by the multiple antigen-binding molecule (α) upon cleavage of the cancer tissue-specific protease-cleavable linker (β). It is preferably, however, a range where damage to normal cells is avoided as much as possible.

Cancer tissue-specific proteases may be a single type alone or a combination of two or more types. The number of types of cancer tissue-specific proteases can be appropriately set by those skilled in the art by considering the types of cancers subjected to treatment.

In view of the above, preferred cancer tissue-specific proteases among the proteases presented as examples above are metalloproteinases, and while MMP-2 and MMP-9 are preferred among the metalloproteinases, MMP-2 is more preferred.

A target sequence is a specific amino acid sequence that is specifically recognized by a cancer tissue-specific protease when the target polypeptide is hydrolyzed in an aqueous solution by the cancer tissue-specific protease.

From the viewpoint of reduction of side effects, the target sequence is preferably an amino acid sequence hydrolyzed with high specificity by a cancer tissue-specific protease expressed in a highly tissue-specific manner in cancer tissues to be treated.

Specific target sequences are, for example, target sequences that are specifically hydrolyzed by proteases expressed specifically in cancer tissues presented as examples above, and are disclosed in WO2013/128194, WO2010/081173, WO2009/025846, and such. Alternatively, sequences identified by methods known to those skilled in the art, such as the method described in Nature Biotechnology 19, 661-667 (2001), may be used as the target sequence.

Target sequences are preferably amino acid sequences that are specifically hydrolyzed by MMP-2 which is a preferred cancer tissue-specific protease, as described above. Among the amino acid sequences specifically hydrolyzed by MMP-2, the following amino acid sequence (SEQ ID NO: 9) is preferred: PLGLAG (SEQ ID NO: 9)

The cancer tissue-specific protease-cleavable linkers (β) may be linked to any position of the multiple antigen-binding molecules (α). Considering accessibility to an immune cell antigen-binding region in a multiple antigen-binding molecule (α) by a masking molecule (γ) and producibility of the masking effect on the immune cell antigen-binding region, a cancer tissue-specific protease-cleavable linker (β) is preferably linked to the immune cell antigen-binding region in the multiple antigen-binding molecule (α).

When a multiple antigen-binding molecule (α) is a multispecific antibody, and a cancer antigen-binding region and an immune cell antigen-binding region are formed by different Fv regions, a cancer tissue-specific protease-cleavable linker (β) is preferably fused to the heavy chain N terminus or light chain N terminus of the Fv region (Fab region) on the side that forms the immune cell antigen-binding region (see FIG. 3; those shown in the figure are referred to respectively as “heavy chain N-terminal fusion molecule” and “light chain N-terminal fusion molecule”). When the cancer tissue-specific protease-cleavable linker (β) is fused to the heavy chain N terminus or light chain N terminus of the Fv region on the side that forms the immune cell antigen-binding region, it is not necessary to perform a step of linking the cancer tissue-specific protease-cleavable linker (β) after preparation of the multiple antigen-binding molecule (α), and this provides excellent efficiency of producing multiple antigen-binding molecule fusion molecules. Furthermore, as described later, this also makes it easy to set the amino-acid lengths of the cancer tissue-specific protease-cleavable linker (β) and the masking molecule (γ).

Cancer tissue-specific protease-cleavable linkers (β) can be obtained, for example, by known methods for producing polypeptides.

Masking Molecule (γ)

A masking molecule (γ) comprises a polypeptide consisting of the amino acid sequence QDGNE. The polypeptide consisting of the amino acid sequence QDGNE is a human CD3ε partial peptide which is derived from human CD3ε.

The masking molecules (γ) mask the immune cell antigen-binding regions of the multiple antigen-binding molecules (α) in multiple antigen-binding molecule fusion molecules and thus have a function to prevent the binding of the immune cell antigen-binding regions to immune cell antigens. Masking of an immune cell antigen-binding region by a masking molecule (γ) may take place intermolecularly between multiple antigen-binding molecule fusion molecules, and these multiple antigen-binding molecule fusion molecules may be in the form of a complex. The function can be exhibited under such state as well.

In cancer tissues, the above-described cancer tissue-specific protease-cleavable linkers (β) are cleaved by cancer tissue-specific proteases expressed in the cancer tissues. Consequently, the masking molecules (γ) become dissociable from the multiple antigen-binding molecules (α). When the masking molecules (γ) dissociate from the multiple antigen-binding molecule fusion molecules, the immune cell antigen-binding regions of the multiple antigen-binding molecules (α) become capable of binding to immune cell antigens.

On the other hand, in normal tissues, cancer tissue-specific proteases are not expressed, or even if they are expressed, their concentrations are low; thus, under such an environment where the cancer tissue-specific protease-cleavable linkers (β) are unlikely to be cleaved, the masking molecules (γ) cannot dissociate from the multiple antigen-binding molecules (α), and the masking effect on the immune cell antigen-binding regions is maintained. That is, in normal tissues, the masking molecules (γ) bind to the multiple antigen-binding molecules (α) via the cancer tissue-specific protease-cleavable linkers (β) to thereby mask the immune cell antigen-binding regions, which makes it difficult to recruit immune cells; and therefore, side effects caused by the multiple antigen-binding molecules (α) is reduced.

The masking molecules (γ) may or may not have an amino acid sequence other than the amino acid sequence QDGNE. In either case, they can sufficiently exhibit the masking effects under the conditions where the cancer tissue-specific protease-cleavable linkers (β) are not cleaved, and they easily dissociate from the multiple antigen-binding molecules (α) under the conditions where the cancer tissue-specific protease-cleavable linkers (β) have been cleaved.

From the viewpoint of improving the stability of the masking molecules (γ) and preventing the masking effect from being reduced due to binding with CD3γ or CD3ε, the masking molecules (γ) preferably do not have an amino acid sequence other than the amino acid sequence QDGNE.

When the masking molecules (γ) contain an amino acid sequence other than the amino acid sequence QDGNE, they are preferably human CD3ε partial polypeptides. In terms of improving the stability of the masking molecules (γ) and in terms of preventing the masking effects from being reduced due to binding with CD3γ or CD3ε, a human CD3ε partial polypeptide is preferably a linear peptide (linear epitope) to which an immune cell antigen-binding region may bind. Use of a linear peptide can suppress an increase of the molecular weight of the multiple antigen-binding molecule fusion molecules, suppress an increase of the dose, and reduce the burden on the patients.

Specifically, the human CD3ε partial polypeptide is preferably a human CD3εpartial polypeptide having the amino acid sequence QDGNE at the N terminus and containing 30 or fewer amino acids, more preferably a human CD3ε partial polypeptide having the amino acid sequence QDGNE at the N terminus and containing 25 or fewer amino acids, even more preferably a human CD3ε partial polypeptide having the amino acid sequence QDGNE at the N terminus and containing 20 or fewer amino acids, particularly preferably a human CD3ε partial polypeptide having the amino acid sequence QDGNE at the N terminus and containing 15 or fewer amino acids, and most preferably a human CD3ε partial polypeptide having the amino acid sequence QDGNE at the N terminus and containing ten or fewer amino acids.

The masking molecules (γ) may be chemically modified. The chemical modifications may be known modifications. Examples of the chemical modifications include acetylation, alkylation, and pyroglutamylation. Among the modifications, pyroglutamylation of Q in the amino acid sequence QDGNE is preferred.

The masking molecules (γ) are obtained by a known method for producing polypeptides. Furthermore, when it is chemically modified, modifications can be carried out by known methods for chemical modification of polypeptides.

Amino Acid Lengths of a Cancer Tissue-Specific Protease-Cleavable Linker (13) and a Masking Molecule (γ)

When a cancer tissue-specific protease-cleavable linker (β) and a masking molecule (γ) constitute a linear fusion polypeptide, the total amino acid length of the cancer tissue-specific protease-cleavable linker (β) and the masking molecule (γ) may be optimized to sufficiently obtain the masking effect of the masking molecule (γ) on the immune cell antigen-binding region.

When the cancer tissue-specific protease-cleavable linker (β) is fused to the heavy-chain N-terminus of the Fv region that forms the immune cell antigen-binding region (upper panel in FIG. 3), the number of amino acids of the fusion polypeptide is preferably eleven or more to 65 or less, more preferably 14 or more to 27 or less, and most preferably 17 or more to 20 or less.

When the cancer tissue-specific protease-cleavable linker (β) is fused to the light-chain N-terminus of the Fv region that forms the immune cell antigen-binding region (lower panel in FIG. 3), the number of amino acids in the fusion polypeptide is preferably 16 or more to 65 or less, more preferably 17 or more to 30 or less, and most preferably 19 or more to 25 or less.

Methods for Producing a Multiple Antigen-Binding Molecule Fusion Molecule

Examples of methods for producing multiple antigen-binding molecule fusion molecules include a method in which a multiple antigen-binding molecule (α), a cancer tissue-specific protease-cleavable linker (β), and a masking molecule (γ) are prepared individually, and the multiple antigen-binding molecule (α) and the masking molecule (γ) are bonded to the cancer tissue-specific protease-cleavable linker (β).

The types of bonds used in this method are not particularly limited so long as the multiple antigen-binding molecule (α) and the masking molecule (γ) are chemically bonded to the cancer tissue-specific protease-cleavable linker (β). Among chemical bonds, covalent bonds are preferred, and covalent bonds formed by peptide bonds are more preferred.

In addition to this method, when the multiple antigen-binding molecule fusion molecules are fusion proteins or an assembly of fusion proteins which may be glycosylated, the multiple antigen-binding molecule fusion molecules may be produced by a known protein expression method, for example, a method that uses host cells and an expression vector in combination.

In the case of using eukaryotic cells as the host cells, animal cells, plant cells, or fungus cells can be appropriately used. Specifically, examples of the animal cells can include the following cells:

-   -   (1) mammalian cells: CHO (Chinese hamster ovary cell line), COS         (monkey kidney cell line), myeloma (Sp2/O, NS0, etc.), BHK (baby         hamster kidney cell line), HEK293 (human embryonic kidney cell         line with sheared adenovirus (Ad)5 DNA), PER.C6 cell (human         embryonic retinal cell line transformed with the Adenovirus Type         5 (Ad5) E1A and E1B genes), Hela, and Vero, or such (Current         Protocols in Protein Science (May, 2001, Unit 5.9, Table         5.9.1));     -   (2) amphibian cells: Xenopus oocytes or such; and     -   (3) insect cells: sf9, sf21, Tn5, or such.

The multiple antigen-binding molecule fusion molecules can also be prepared using E. coli (mAbs 2012 March-April; 4 (2): 217-225) or yeast (WO2000/023579). Multiple antigen-binding molecule fusion molecules prepared using E. coli are not glycosylated. On the other hand, multiple antigen-binding molecule fusion molecules prepared using yeast are glycosylated.

Expression vectors may be suitably selected by the skilled artisan depending on the type of host cells.

The multiple antigen-binding molecule fusion molecules can be collected, for example, by culturing transformed cells and then separating the multiple antigen-binding molecule fusion molecules from within the molecule-transformed cells or from the culture media. The multiple antigen-binding molecule fusion molecules can be separated and purified by appropriately using in combination methods such as centrifugation, ammonium sulfate fractionation, salting out, ultrafiltration, C1q, FcRn, protein A and protein G columns, affinity chromatography, ion-exchange chromatography, and gel filtration chromatography.

The techniques mentioned above, such as the knobs-into-holes technology (WO1996/027011; Ridgway J B et al., Protein Engineering (1996) 9, 617-621; and Merchant A M et al., Nature Biotechnology (1998) 16, 677-681) or the technique of suppressing unintended association between H chains by introduction of electric charge repulsion (WO2006/106905 and WO2015/046467), can be applied as methods for efficiently preparing the multiple antigen-binding molecule fusion molecules.

B. Pharmaceutical Compositions

Pharmaceutical compositions of the present invention contain an above-mentioned multiple antigen-binding molecule fusion molecule and a pharmaceutically acceptable carrier. Pharmaceutical compositions can be made to contain an above-mentioned multiple antigen-binding molecule fusion molecule and a pharmaceutically acceptable carrier, and can be formulated by known methods.

For example, the pharmaceutical compositions can be used in the form of a parenteral injection of an aseptic solution or suspension with water or any other pharmaceutically acceptable solution. For example, the pharmaceutical compositions may be formulated by mixing the molecule in a unit dosage form required for generally accepted pharmaceutical practice in appropriate combination with a pharmacologically acceptable carrier or medium, specifically, sterilized water, physiological saline, plant oil, an emulsifier, a suspending agent, a surfactant, a stabilizer, a flavoring agent, an excipient, a vehicle, a preservative, a binder, or such. Specific examples of the carrier include light anhydrous silicic acid, lactose, crystalline cellulose, mannitol, starch, carmellose calcium, carmellose sodium, hydroxypropylcellulose, hydroxypropylmethylcellulose, polyvinyl acetal diethylaminoacetate, polyvinylpyrrolidone, gelatin, medium-chain fatty acid triglyceride, polyoxyethylene hydrogenated castor oil 60, saccharose, carboxymethylcellulose, cornstarch, and inorganic salts. The amount of active ingredients in these formulations is adjusted to achieve an appropriate dose within a prescribed range.

An aseptic composition for injection can be formulated according to conventional pharmaceutical practice using a vehicle such as injectable distilled water. Examples of aqueous solutions for injection include physiological saline, isotonic solutions containing glucose and other adjuvants, for example, D-sorbitol, D-mannose, D-mannitol, and sodium chloride. These solutions may be used in combination with an appropriate solubilizer, for example, an alcohol (specifically, ethanol) or a polyalcohol (e.g., propylene glycol and polyethylene glycol), or a nonionic surfactant, for example, polysorbate 80 or HCO-50.

Examples of oily solutions include sesame oil and soybean oil. These solutions may be used in combination with benzyl benzoate or benzyl alcohol as a solubilizer. The solutions may be further mixed with a buffer (e.g., a phosphate buffer solution and a sodium acetate buffer solution), a soothing agent (e.g., procaine hydrochloride), a stabilizer (e.g., benzyl alcohol and phenol), or an antioxidant. The injection solutions thus prepared are usually charged into appropriate ampules.

A preferred administration is parenteral administration, and specific examples of dosage forms include injections, intranasal administration agents, transpulmonary administration agents, and percutaneous administration agents. Examples of injections include intravenous injection, intramuscular injection, intraperitoneal injection, and subcutaneous injection, through which systemic or local administration can be done.

The administration method can be appropriately selected depending on the age and symptoms of a patient. The dose of the pharmaceutical composition containing a multiple antigen binding molecule fusion molecule and a pharmaceutically acceptable carrier can be selected within a range of, for example, 0.0001 to 1000 mg/kg of body weight per dose. Alternatively, the dose can be selected within a range of, for example, 0.001 to 100000 mg/body of a patient, though the dose is not necessarily limited to these numeric values. Although the dose and the administration method vary depending on the weight, age, symptoms, and such of a patient, those skilled in the art can appropriately select the dose and the method.

The pharmaceutical compositions are preferably for cancer treatment. Preferably, cancer types to be treated specifically express cancer antigens recognized by the cancer antigen-binding regions in the multiple antigen-binding molecules (α) included in the multiple antigen-binding molecule fusion molecules to be used. The cancer types to be treated may be solid cancers or blood cancers.

The pharmaceutical compositions of the present invention can provide methods for treating cancer which comprise administering the pharmaceutical compositions to patients.

C. Methods for Identifying Linear Epitopes

Methods for identifying a linear epitope of the present invention comprise a step of identifying, based on three-dimensional protein structure analysis data obtained by using a protein complex formed between an immune cell antigen and an immune cell antigen-binding region that recognizes the immune cell antigen, a linear epitope included in the immune cell antigen and recognized by the immune cell antigen-binding region.

The immune cell antigen-binding region, depending on the type thereof, may recognize a linear peptide portion in an immune cell antigen or may recognize a higher-order structure portion of a polypeptide forming a higher-order structure. The method for identifying a linear epitope of the present invention is a method for identifying a linear peptide to which the immune cell antigen-binding region is capable to bind, where the immune cell antigen-binding region recognizes a linear peptide portion in an immune cell antigen.

The identified linear peptides are useful as a masking molecule (γ) which does not require the formation of a higher-order structure. Since linear peptides do not require formation of higher-order structures, they can stably exhibit a masking effect.

D. Methods for Producing Multiple Antigen-Binding Molecule Fusion Molecules

Methods for producing multiple antigen-binding molecule fusion molecules of the present invention comprise a step of expressing a fusion protein in which a linear epitope (for example, a linear epitope identified by the above-mentioned method for identifying linear epitopes) is fused to a multiple antigen-binding molecule (α) containing a cancer antigen-binding region which recognizes a cancer antigen and an immune cell antigen-binding region which recognizes an immune cell antigen via a cancer tissue-specific protease-cleavable linker (β) containing a region that may be cleaved by a protease specifically expressed in a cancer tissue expressing said cancer antigen.

The multiple antigen-binding molecules (α) and the cancer tissue-specific protease-cleavable linkers (β) are the same as those described above under “A. Multiple antigen-binding molecule fusion molecules”.

The linear epitope is not particularly limited, but is acceptable if it satisfies the definition given herein.

The linear epitope may be a linear epitope identified by the above-described method for identifying a linear epitope, or it may be one identified by such known epitope mapping methods that ELISA, mass spectrometry, phage library, and such are performed using partial peptides of various antigens. The linear epitope is preferably a linear epitope identified by the above-mentioned method for identifying linear epitopes from the viewpoint that the binding state between an immune cell antigen and the immune cell antigen-binding region can be analyzed in detail and with accuracy to thereby obtain a minimal unit of the epitope, and from the viewpoint that acquisition of a minimal unit of the epitope makes it possible to obtain a multiple antigen-binding molecule fusion molecule that can stably exhibit a masking effect without requiring the formation of higher-order structures.

E. Functional Effects of the Present Invention

The multiple antigen-binding molecule fusion molecules of the present invention are specifically activated by proteases present inside or near cancer tissues, and can recruit immune cells such as T cells to cancer cells. Therefore, the multiple antigen-binding molecules that recognize cancer antigens and CD3 can produce excellent side-effect-reducing effects.

In the multiple antigen-binding molecule fusion molecules of the present invention, masking molecules comprising a polypeptide having the amino acid sequence QDGNE (SEQ ID NO: 15) are used. Such masking molecules only need to carry at least a polypeptide consisting of the amino acid sequence QDGNE (SEQ ID NO: 15), and are easily produced due to their smaller molecular weight as compared to the masking molecule disclosed in WO2013/128194. Because the molecular weight of the masking molecules can be lowered, the molecular weight of the multiple antigen-binding molecule fusion molecules can be lowered, the dose can be decreased, and the burden on the patients can be reduced.

CD3ε is generally known to form a homodimer or a heterodimer with CD3γ or CD3ε (Scand. J. Immunol. 2002 Vol. 56, pp. 436-442). Therefore, the stability of CD3ε or a partial protein of CD3ε may be lowered when it exits as a monomer. Furthermore, when CD3ε or a partial protein of CD3ε is used as a masking molecule, it may readily form a dimer with each other or with endogenous proteins, and a sufficient masking effect may not be readily obtained.

On the other hand, since the masking molecules in the multiple antigen-binding molecule fusion molecules of the present invention only need to have at least a polypeptide consisting of the amino acid sequence QDGNE (SEQ ID NO: 15), they have excellent stability and masking effects.

The epitope of the antigen-binding region of OKT3, which is an anti-CD3ε antibody used in WO2013/128194, is not shared between humans and cynomolgus monkeys. Therefore, OKT3 is an antibody specific to human CD3ε, and it has not been found to bind to cynomolgus CD3ε. Because of this, non-clinical toxicity tests using cynomolgus monkeys cannot be carried out, or even if non-clinical toxicity tests using cynomolgus monkeys were carried out, they would not reflect the results of clinical trials.

In contrast, the amino acid sequence QDGNE (SEQ ID NO: 15) in an antigen recognized by the immune cell antigen-binding regions of the present invention is the same in humans and cynomolgus monkeys. Therefore, the test results obtained in non-clinical toxicity tests using cynomolgus monkeys will be likely to reflect the results of clinical trials.

All references cited herein are incorporated herein by reference in their entirety.

Those skilled in the art should understand that one of or any combination of two or more of the aspects described herein is also included in the present invention unless a technical contradiction arises on the basis of the technical common sense of those skilled in the art.

EXAMPLES

The present invention will be further illustrated with reference to Examples below. However, the present invention is not intended to be limited by Examples below.

Example 1: Concept of an Anti-Cancer Antigen/Anti-CD3 Multiple Antigen-Binding Molecule Fusion Molecule Activated by a Protease

Anti-cancer antigen/anti-CD3 multiple antigen-binding molecule is expected to be a promising molecular format of anti-cancer agents due to its potent cytotoxic activity, but on the other hand, if the cancer antigen is expressed even slightly in normal tissues, the molecule may exhibit a damaging activity on the normal tissues as well; therefore, anti-cancer antigen/anti-CD3 multiple antigen-binding molecules with few side effects and having superior safety properties are desired. In this regard, if an anti-cancer antigen/anti-CD3 multiple antigen-binding molecule can be derivatized to produce an anti-cancer antigen/anti-CD3 multiple antigen-binding molecule fusion molecule which is activated by proteases, an anti-cancer antigen/anti-CD3 multiple antigen-binding molecule with few side effects and superior safety properties can be prepared easily (FIG. 2).

For the protease-activatable anti-cancer antigen/anti-CD3 multiple antigen-binding molecule fusion molecules to have further reduced side effects and superior safety properties, it is preferable that the molecules have the following three structural features. The first feature is that a masking molecule (γ) which inhibits the binding activity of an anti-CD3 antibody is linked to the heavy-chain N terminus or the light-chain N terminus of an anti-CD3 antibody variable region via a cancer tissue-specific protease-cleavable linker (β). The second feature is that the masking molecule (γ) is comprised of a naturally-occurring epitope sequence of the anti-CD3 antibody and does not contain any non-natural sequence from the viewpoint of immunogenicity, and homology of the corresponding amino acid sequences between species (for example, between human and cynomolgus monkey) is high. The third feature is that the cancer tissue-specific protease-cleavable linker (β) contains a target sequence that is cleaved by a protease present at high concentration inside or near cancer tissues.

Reference Example 1: Preparation of Anti-Human and Anti-Cynomolgus Monkey CD3ε Antibody “CE115”

1-1. Preparation of Hybridoma Using Rat Immunized with Cell Expressing Human CD3 and Cell Expressing Cynomolgus Monkey CD3

Each SD rat (female, 6 weeks old at the start of immunization, Charles River Laboratories Japan, Inc.) was immunized with Ba/F3 cells expressing human CD3εγ or cynomolgus monkey CD3εγ as follows: at day 0 (the priming date was defined as day 0), 5×10⁷ Ba/F3 cells expressing human CD3εγ were intraperitoneally administered together with a Freund complete adjuvant (Difco Laboratories, Inc.) to the rat. At day 14, 5×10⁷ Ba/F3 cells expressing cynomolgus monkey CD3εγ were intraperitoneally administered together with a Freund incomplete adjuvant (Difco Laboratories, Inc.). Then, 5×10⁷ Ba/F3 cells expressing human CD3εγ and Ba/F3 cells expressing cynomolgus monkey CD3εγ were intraperitoneally administered thereto a total of four times every other week in an alternate manner. One week after (at day 49) the final administration of CD3εγ, Ba/F3 cells expressing human CD3εγ were intravenously administered as a booster. Three days thereafter, spleen cells of the rats were fused with mouse myeloma cells SP2/0 according to a conventional method using PEG1500 (Roche Diagnostics K.K.). Fusion cells, i.e., hybridomas, were cultured in an RPMI1640 medium containing 10% FBS (hereinafter, referred to as 10% FBS/RPMI1640).

On the day after the fusion, (1) the fusion cells were suspended in a semifluid medium (Stem cell Technologies, Inc.). The hybridomas were selectively cultured and also colonized.

Nine or ten days after the fusion, hybridoma colonies were picked up and inoculated at 1 colony/well to a 96-well plate containing a HAT selective medium (10% FBS/RPMI1640, 2 vol % HAT 50×concentrate (Sumitomo Dainippon Pharma Co., Ltd.), and 5 vol % BM-Condimed H1 (Roche Diagnostics K.K.)). After 3- to 4-day culture, the culture supernatant in each well was recovered, and the rat IgG concentration in the culture supernatant was measured. The culture supernatant confirmed to contain rat IgG was screened for a clone producing an antibody specifically binding to human CD3εγ by cell-ELISA using attached Ba/F3 cells expressing human CD3εγ or attached Ba/F3 cells expressing no human CD3εγ (FIG. 4). The clone was also evaluated for cross-reactivity with monkey CD3εγ by cell-ELISA using attached Ba/F3 cells expressing cynomolgus monkey CD3εγ (FIG. 4).

1-2. Preparation of Anti-Human and Anti-Monkey CD3ε Chimeric Antibody

Total RNA was extracted from each hybridoma cells using RNeasy Mini Kits (Qiagen N.V.), and cDNA was synthesized using SMART RACE cDNA Amplification Kit (BD Biosciences). The prepared cDNA was used in PCR to insert the antibody variable region gene to a cloning vector. The nucleotide sequence of each DNA fragment was determined using BigDye Terminator Cycle Sequencing Kit (Applied Biosystems, Inc.) and a DNA sequencer ABI PRISM 3700 DNA Sequencer (Applied Biosystems, Inc.) according to the method described in the instruction manual included therein. CDRs and FRs of the CE115 H chain variable domain and the CE115 L chain variable domain were determined according to the Kabat numbering.

A rat anti-CD3 antibody comprising a heavy chain variable region (SEQ ID NO: 10) and a light chain variable region (SEQ ID NO: 11) as well as a humanized anti-CD3 antibody comprising a heavy chain variable region (SEQID NO: 12) and a light chain variable region (SEQ ID NO: 13), which was humanized using a method known to those skilled in the art, were prepared.

Reference Example 2: Preparation of Antibody Expression Vector and Expression and Purification of Antibody

Amino acid substitutions was carried out by a method generally known to those skilled in the art using QuikChange Site-Directed Mutagenesis Kit (Stratagene Corp.), PCR, or In fusion Advantage PCR cloning kit (Takara Bio Inc.), etc., to construct expression vectors. The obtained expression vectors were sequenced by a method generally known to those skilled in the art. The prepared plasmids were transiently transferred to human embryonic kidney cancer cell-derived HEK293H line (Invitrogen Corp.) or FreeStyle 293 cells (Invitrogen Corp.) to express antibodies. Each antibody was purified from the obtained culture supernatant by a method generally known to those skilled in the art using rProtein A Sepharose (registered trademark) Fast Flow (GE Healthcare Japan Corp.). As for the concentration of the purified antibody, the absorbance was measured at 280 nm using a spectrophotometer, and the antibody concentration was calculated by use of an extinction coefficient calculated from the obtained value by PACE (Protein Science 1995; 4: 2411-2423).

Example 2: X-Ray Crystallographic Analysis of a Complex Formed Between Anti-CD3 Antibody and CD3

An anti-CD3 antibody consisting of a heavy chain (variable region (SEQ ID NO: 12) and a constant region (SEQ ID NO: 38)), a light chain (variable region (SEQ ID NO: 13) and a constant region (SEQ ID NO: 36)), and Kn010G3 (SEQ ID NO: 37) was expressed and prepared as a One-arm antibody by the method of Reference Example 1. Anti-CD3 antibody Fab fragment was prepared from the obtained One-arm antibody by performing cleavage treatment using papain protease (Roche Applied Science), removal of Fc fragments using a Protein A column, and purification using a cation exchange column and a gel filtration column, according to methods known to those skilled in the art.

The obtained anti-CD3 antibody Fab fragment was concentrated by ultrafiltration, and crystals were obtained by the vapor diffusion method, in which the Fab fragment was left to stand at 20° C. under reservoir conditions of 200 mM Potassium Sulfate and 20% PEG3350. X-ray crystallography was performed using the obtained crystals based on known Fab fragment crystal structures according to a method known to those skilled in the art to obtain the crystal structure of the anti-CD3 antibody Fab fragment alone from the diffraction intensity data at 25 to 2.12 angstrom resolution. Its crystallographic reliability factor R (R factor) and Free R value (R free) were 22.21% and 26.28%, respectively.

Furthermore, a sample was prepared by adding, to the obtained anti-CD3 antibody Fab fragment, a synthetic peptide (epitope peptide) which corresponds to the sequence from the N terminus to position 15 of CD3 and shown in SEQ ID NO: 14 below: XDGNEEMGGITQTPY (X: L-pyroglutamic acid) (SEQ ID NO: 14) to become 2 mM. The vapor diffusion method was used to obtain crystals from the sample by allowing the sample to stand at 20° C. under reservoir conditions of 100 mM MES buffer at pH7.0, 0.91% PEG3350, and 1.0 M sodium citrate tribasic dihydrate. These crystals were subject to X-ray crystallography based on the above-mentioned crystal structure of the anti-CD3 antibody Fab fragment alone according to a method known to those skilled in the art to obtain the crystal structure of a complex of the anti-CD3 antibody Fab fragment and the epitope peptide from the diffraction intensity data at 25 to 3.5 angstrom resolution. Its crystallographic reliability factor R (R factor) and Free R value (R free) were 18.55% and 26.53%, respectively.

The structure and electron density map near the epitope in the complex formed by the anti-CD3 antibody Fab fragment and the epitope peptide based on the obtained crystal structure are shown in FIG. 5. The electron density was sufficiently observed only from the N terminus to the fifth residue Glu of the epitope peptide; therefore, a model could not be constructed for the sequence from the sixth residue of the epitope peptide and beyond. Thus, this antibody was found to bind to CD3 by mainly recognizing the peptide sequence from the N terminus to the fifth residue of CD3 (epitope core sequence), at the pocket formed between the heavy and light chains of the Fab fragment (see the arrow in FIG. 1).

Since the epitope core sequence on CD3 for the above-mentioned antibody could be identified in this manner, an appropriate linker length for linking this epitope core sequence with the anti-CD3 antibody heavy chain N terminus and an appropriate linker length for linking this epitope core sequence with the anti-CD3 antibody light chain N terminus were estimated using the MOE program (Chemical Computing Group Inc.).

First, based on the obtained crystal structure of the complex of the Fab fragment and the epitope peptide, two models were produced: one model in which Gly was added to each of the heavy chain N terminus and the C terminus of the fifth residue Glu of the epitope peptide; and the other model in which Gly was added to each of the light chain N terminus and the C terminus of the fifth residue Glu of the epitope peptide.

Next, to search for Gly linkers for linking the added Gly residues to each other, hydrogen atoms were added to both models using the protonate 3D function, AMBER10: EHT was used as the force field, solvation R-field was specified for solvation, and Linker modeler function was used for sampling from the Protein Data Bank database using lengths of 1 to 60 residues as the searching range.

As a result, when linking the epitope core sequence and the anti-CD3 antibody heavy-chain N terminus using a linker, the minimum length for the linkage was suggested to be a six-amino-acid linker (FIG. 6A). However, a linker consisting of six amino acid residues follows a path that nearly contacts the antibody surface, and when linkage is attempted by using for example a linker containing amino acids other than Gly, steric hindrance with the antibody is expected to occur. On the other hand, as shown in FIGS. 6B, 6C, and 6D, when a linker consisting of 9, 12, or 16 amino acids is used for the linkage, some room is formed between the linker and the antibody surface, and it is expected that even a linker containing residues other than Gly would be used for the linkage.

Similarly, when linking the epitope core sequence and the anti-CD3 antibody light-chain N terminus using a linker, the minimum length for the linkage was suggested to be an eleven-amino-acid linker (FIG. 7A). However, a linker consisting of eleven amino acid residues follows a path that nearly contacts the antibody surface, and when linkage is attempted by using for example a linker containing amino acids other than Gly, steric hindrance with the antibody is expected to occur. On the other hand, as shown in FIGS. 7B, 7C, and 7D, when a linker consisting of 12, 14, or 16 amino acids is used for the linkage, some room is formed between the linker and the antibody surface, and it is expected that a linker containing residues other than Gly would be used for the linkage.

From the above results, when linking the epitope sequence and the anti-CD3 antibody heavy-chain N terminus (top panel of FIG. 3), the appropriate amino acid lengths of the cancer tissue-specific protease-cleavable linker (β) and the masking molecule (γ) were estimated to be 11 amino acids or more to 65 amino acids or less, more preferably 14 to 27 amino acids, and even more preferably 17 to 20 amino acids.

Furthermore, when linking the epitope sequence and the anti-CD3 antibody light-chain N terminus (bottom panel of FIG. 3), the appropriate amino acid lengths of the cancer tissue-specific protease-cleavable linker (β) and the masking molecule (γ) were estimated to be 16 amino acids or more to 65 amino acids or less, more preferably 17 to 30 amino acids, and even more preferably 19 to 25 amino acids.

Example 3: Preparation of an Anti-CD3 Antibody Derivative in which Binding to CD3ε is Masked

As indicated in Table 1 shown below, anti-CD3 antibody derivatives in which a masking molecule (γ) and a cancer tissue-specific protease-cleavable linker (β) have been fused to the heavy chain N terminus of the humanized anti-CD3 antibody prepared in Reference Example 1 are prepared. The cancer tissue-specific protease-cleavable linkers (β) used in Table 1 have a sequence targeted by MMP-2 (WO2010/081173 and WO2009/025846), and are peptides that have different lengths. The targeted sequence is known to be cleaved by MMP-9 as well (Integr Biol (Camb). 2009 June; 1(5-6): 371-381).

TABLE 1 Cancer tissue- Antibody specific protease variable region + Full-length Full-length Antibody Masking cleavable linker constant heavy chain light chain Name molecule (γ) (β) region sequence sequence CD3H1 SEQ ID NO: 15 SEQ ID NO: 16 SEQ ID NO: 20 SEQ ID NO: 21 SEQ ID NO: 25 CD3H2 SEQ ID NO: 15 SEQ ID NO: 17 SEQ ID NO: 20 SEQ ID NO: 22 SEQ ID NO: 25 CD3H3 SEQ ID NO: 15 SEQ ID NO: 18 SEQ ID NO: 20 SEQ ID NO: 23 SEQ ID NO: 25 CD3H4 SEQ ID NO: 15 SEQ ID NO: 19 SEQ ID NO: 20 SEQ ID NO: 24 SEQ ID NO: 25

Moreover, as indicated in Table 2, anti-CD3 antibody derivatives in which a masking molecule (γ) and a cancer tissue-specific protease-cleavable linker (β) have been fused to the light chain N terminus of the humanized anti-CD3 antibody prepared in Reference Example 1 are prepared. As in Table 1, the cancer tissue-specific protease-cleavable linkers (13) used in the table have a sequence targeted by MMP-2 (WO2010/081173 and WO2009/025846), and are peptides that have different lengths. The targeted sequence is known to be cleaved by MMP-9 as well (Integr. Biol. (Camb.) 2009 June; 1 (5-6): 371-381).

TABLE 2 Cancer tissue- Antibody specific protease variable region + Full-length Full-length Antibody Masking cleavable linker constant light chain heavy chain Name molecule (γ) (β) region sequence sequence CD3L1 SEQ ID NO: 15 SEQ ID NO: 26 SEQ ID NO: 29 SEQ ID NO: 30 SEQ ID NO: 34 CD3L2 SEQ ID NO: 15 SEQ ID NO: 27 SEQ ID NO: 29 SEQ ID NO: 31 SEQ ID NO: 34 CD3L3 SEQ ID NO: 15 SEQ ID NO: 28 SEQ ID NO: 29 SEQ ID NO: 32 SEQ ID NO: 34 CD3L4 SEQ ID NO: 15 SEQ ID NO: 19 SEQ ID NO: 29 SEQ ID NO: 33 SEQ ID NO: 34

CD3H1, CD3H2, CD3H3, and CD3H4 of Table 1 and CD3L1, CD3L2, CD3L3, and CD3L4 of Table 2 are prepared by known antibody production methods using the respective plasmid encoding the heavy chain full-length sequence and expression vector carrying the light chain full-length sequence.

Example 4: Assessment of Binding Between CD3 and the Anti-CD3 Antibody

An anti-CD3 antibody was prepared according to the method of Reference Example 2. Specifically, first, an animal cell expression vector for expression of a polypeptide in which the heavy chain variable region (SEQ ID NO: 10) and pE22Hh (SEQ ID NO: 35) have been fused, an animal cell expression vector for expression of a polypeptide in which the light chain variable region (SEQ ID NO: 11) and Kappa chain (SEQ ID NO: 36) have been fused, and an animal cell expression vector for expression of the heavy chain constant region ranging from the hinge portion to the C-terminal side (Kn0101G3 (SEQ ID NO: 37)), were used to coexpress these polypeptides in cells to produce an anti-CD3 antibody as a One-arm antibody. Then, the anti-CD3 antibody was purified from the culture supernatant.

Assessment of binding between the anti-CD3 antibody and human CD3 was performed using BiacoreT200. Specifically, biotinylated CD3 peptide was bound to a CM4 chip via streptavidin, the prepared antibody was flushed as the analyte, and the binding affinity was analyzed at 37° C.

The results of evaluation of binding are shown in Table 3 below.

TABLE 3 sample ka (1/Ms) kd (1/s) KD (M) Anti-CD3 antibody 1.09E+05 4.19E−02 3.83E−07

Reference Example 3: Selection of Anti-CD3 Antibody Derivatives Having Enhanced Binding to CD3ε Reference Example 3-1. Method for Enhancing CD3 Binding

A possible method using the anti-CD3 antibody-derived antibody library (Dual Fab Library) described in WO2015/068847 is a method for obtaining an antibody having increased binding to CD3. General examples of affinity maturation include a method which involves altering an amino acid in an obtained antibody sequence by site-directed mutagenesis and measuring affinity, and methods using in vitro display methods including phage display. In the in vitro display methods, plural types of antibody sequences mutated from an obtained sequence by error prone PCR or the like are used as a library to select a sequence having strong affinity.

Use of a dual-Fab library containing selected amino acids that maintain 80% or more of the CD3 binding of a conventional anti-CD3 antibody (e.g., a CD3-binding antibody having the template sequence mentioned above) may allow the efficient finding of a sequence having strong binding to CD3.

Reference Example 3-2: Obtainment of Fab Domain Having Enhanced Binding to Human CD3

Fab domains (antibody fragments) binding to human CD3 were identified from the dual Fab library disclosed in WO2015/068847. Biotin-labeled CD3 was used as an antigen, and antibody fragments having the ability to bind to human CD3 were enriched.

Phages were produced from the E. coli harboring the constructed phagemids for phage display. 2.5 M NaCl/10% PEG was added to the culture solution of the E. coli that had produced phages, and a pool of the phages thus precipitated was diluted with TBS to obtain a phage library solution. Next, BSA (final concentration: 4%) was added to the phage library solution. The panning method was performed with reference to a general panning method using antigens immobilized on magnetic beads (J. Immunol. Methods. (2008) 332 (1-2), 2-9; J. Immunol. Methods. (2001) 247 (1-2), 191-203; Biotechnol. Prog. (2002) 18 (2) 212-20; and Mol. Cell Proteomics (2003) 2 (2), 61-9). The magnetic beads used were NeutrAvidin coated beads (Sera-Mag SpeedBeads NeutrAvidin-coated) or Streptavidin coated beads (Dynabeads M-280 Streptavidin).

Specifically, 250 pmol of the biotin-labeled antigen was added to the prepared phage library solution and thereby contacted with the phage library solution at room temperature for 60 minutes. After addition of BSA-blocked magnetic beads, the antigen-phage complexes were attached to the magnetic beads at room temperature for 15 minutes. The beads were washed three times with TBST (TBS containing 0.1% Tween 20; TBS was available from Takara Bio Inc.) and then further washed twice with 1 mL of TBS. After addition of 0.5 mL of 1 mg/mL trypsin, the beads were suspended at room temperature for 15 minutes, immediately after which the beads were separated using a magnetic stand to recover a phage solution. The recovered phage solution was added to 10 mL of an E. coli strain ER2738 in a logarithmic growth phase (OD600: 0.4-0.5). The E. coli strain was infected by the phages through the gentle spinner culture of the strain at 37° C. for 1 hour. The infected E. coli was inoculated to a plate of 225 mm×225 mm. Next, phages were recovered from the culture solution of the inoculated E. coli to prepare a phage library solution. This cycle, called panning, was repeated 7 times in total. In the second and subsequent rounds of panning, 40, 10, 10, 1, 1, and 0.1 pmol of the human CD3 were respectively used. In the fifth and subsequent rounds, a 1000-fold amount of a human CD3ε homodimer was added each time the human CD3 was added.

Reference Example 3-3: Preparation of IgG Having the Obtained Fab Domain

The population of antibody fragments having the ability to bind to CD3 obtained in Reference Example 3-2 is constituted by only Fab domains. Thus, these Fab domains were converted to IgG type (conjugate of Fab and Fc). The VH fragment was amplified from E. coli, each having an antibody fragment having the ability to bind to CD3, by PCR using primers specifically binding to the H chain in the dual Fab library. Using the method of Reference Example 2, the amplified VH fragment was integrated into a plasmid, which allows expression in animal cells and, into which F760mnP17 (SEQ ID NO: 39) had been incorporated. Specifically, AN121H-F760mnP17 (SEQ ID NO: 40) was used as an H chain, and a sequence (SEQ ID NO: 25) made by linking GLS3000 (SEQ ID NO: 13) to the kappa sequence (SEQ ID NO: 36) was used as an L chain. These sequences were expressed and purified according to Reference Example 1. This antibody was called AN121.

Example 5: Evaluation of Binding to CD3εδ Heterodimer

Binding of antibodies prepared in the Reference Examples to a CD3εδ heterodimer was evaluated by the surface plasmon method (SPR method).

5-1. Preparation of a CD3εδ Heterodimer

A CD3εδ heterodimer was prepared by the following method. First, to the 3′ end of a gene encoding the extracellular domain of CD3ε, a gene encoding a Factor Xa cleavage site and a gene encoding the amino acids on the C-terminal side from the hinge region of a human immunoglobulin (IgG1) in which position 349 is Cys and position 366 is Trp (EU numbering) were fused, and additionally a gene encoding a TEV protease cleavage site and a BAP tag sequence was fused to produce a gene (a gene encoding SEQ ID NO: 41). The obtained gene was inserted into an animal cell expression vector. Next, to the 3′ end of a gene encoding the extracellular domain of CD3ε, a gene encoding a Factor Xa cleavage site and a gene encoding the C-terminal side from the hinge region of a human immunoglobulin (IgG1) in which position 356 is Cys, position 366 is Ser, position 368 is Ala, and position 407 is Val (EU numbering) were fused, and additionally a gene encoding a Flag tag sequence was fused to produce a gene (a gene encoding SEQ ID NO: 42). The obtained gene was inserted into an animal cell expression vector. As in Reference Example 2, the animal cell expression vector carrying the gene encoding SEQ ID NO: 41 and the animal cell expression vector carrying the gene encoding SEQ ID NO: 42 were introduced into FreeStyle 293 cells (Invitrogen). After the introduction, the cells were shake cultured at 37° C. according to a protocol, and the supernatant was collected five days later. The CD3εδ heterodimer to which an antibody constant region (particularly Fc) had been fused was obtained from the supernatant using a Protein A column (Eshmuno A (Merck)). To further obtain the heterodimer, the CD3F6 heterodimer to which an antibody constant region had been fused was fractionated using an Anti-FLAG M2 column (Sigma). Then, gel filtration chromatography (Superdex200, GE Healthcare) was performed to fractionate and collect the desired CD3εδ heterodimer.

Factor Xa (NEB) was added to the collected CD3ε6, to which the antibody constant region had been fused, to separate the CD3εδ heterodimer and the antibody constant region. Protease removal was carried out by passage through a Benzamidine column (GE Healthcare), and the desired CD3εδ heterodimer was obtained using a Mabselect Sure column (GE Healthcare), ion exchange chromatography (Q sepharose HP, GE Healthcare), and gel filtration chromatography (Superdex 200, GE Healthcare).

5-2. Measurement of Binding to the CD3εδ Heterodimer

The activity of binding to the CD3εδ heterodimer was measured for: the rat anti-CD3 antibody containing as the variable region the heavy chain variable region (SEQ ID NO: 10) and the light chain variable region (SEQ ID NO: 11) described in Reference Example 1; a combination of a human anti-CD3 antibody and a rat anti-CD3 antibody which contains as the variable region a heavy chain variable region (SEQ ID NO: 12) and a light chain variable region (SEQ ID NO: 13) where the light chain has been humanized by a method known to those skilled in the art; a humanized anti-CD3 antibody which contains as the variable region a heavy chain variable region (SEQ ID NO: 12) and a light chain variable region (SEQ ID NO: 13), which have been humanized by a method known to those skilled in the art; and AN121 which contains as the variable region a heavy chain variable region (SEQ ID NO: 43) and a light chain variable region (SEQ ID NO: 13). The heavy chain variable regions were fused with F760mnP17 (SEQ ID NO: 39) used as the constant region and the light chain variable regions were fused with the Kappa chain (SEQ ID NO: 36) used as the constant region, and the antibodies were expressed according to the method of Reference Example 2.

The activity of binding to the CD3ε8 heterodimer was assessed using BiacoreT200. Specifically, Protein G was immobilized onto a CM3 chip by a method known to those skilled in the art, and antibodies to be evaluated were bound to the immobilized Protein G. Then, the CD3εδ heterodimer prepared at 4000, 1000, 250, 62.5, 15.6, and 3.9 nM was bound thereto, and the binding was evaluated using the single cycle kinetics mode. Measurements were taken under conditions of 20 mM ACES, 150 mM NaCl, and pH7.4 at 37° C. The results are shown in Table 4.

TABLE 4 Heavy Light chain chain SEQ SEQ ka kd KD Antibody Name ID NO ID NO (1/Ms) (1/s) (M) CE115VH-F760mnP17/rCE115VL-k0 44 45 4.04E+04 7.71E−03 1.91E−07 (Rat anti-CD3 antibody) Combination of rat anti-CD3 44 25 4.73E+04 1.24E−02 2.62E−07 antibody and human anti-CD3 antibody) (CE115VH-F760mnP17/GLS3000-k0) CE115HA000-F760mnP17/GLS3000-k0 46 25 5.18E+04 2.88E−02 5.56E−07 (Humanized anti-CD3 antibody) AN121H-F760mnP17/GLS3000-k0 40 25 7.47E+04 7.23E−04 9.68E−09 (AN121)

As shown in Table 4, AN121 obtained in Reference Example 3 was shown to have enhanced binding to CD3ε6.

Example 6: Preparation of Anti-CD3 Antibody Derivatives with Masked Binding to CD3ε and Noncleavable Antibodies

Anti-CD3 antibody derivatives in which the binding to CD3ε was masked by the addition of a masking molecule (γ) via a cancer tissue-specific protease-cleavable linker (3), and anti-CD3 antibody derivatives to which the masking molecule (γ) was attached using a noncleavable linker that does not carry the cancer tissue-specific protease-cleavable linker (β)(shown in Table 5) were prepared according to the method of Reference Example 2. The sequence reported in WO2013/163631 (LSGRSDNH; SEQ ID NO: 47) was used as the cancer tissue-specific protease-cleavable linker (β). Sequences in which a sequence cleaved by MMP-2 indicated in Example 3 (PLGLAG; SEQ ID NO: 106) or a linker peptide composed of Gly and Ser is inserted at the site of the cancer tissue-specific protease-cleavable linker (β) were also prepared as controls. Specifically, firstly, an animal cell expression vector for expression of a polypeptide in which a heavy chain variable region and pE22Hh (SEQ ID NO: 35) are fused, an animal cell expression vector for expression of a polypeptide in which a light chain variable region and the Kappa chain (SEQ ID NO: 36) are fused, and an animal cell expression vector for expression of the C-terminal side of the heavy chain constant region from the hinge portion (Kn010 (SEQ ID NO: 48)) were used to coexpress these polypeptides in cells to produce an anti-CD3 antibody as a One-arm antibody. Next, the anti-CD3 antibody was purified from the culture supernatant. Alternatively, F760mnP17 (SEQ ID NO: 39) was linked as the heavy chain constant region to the heavy chain variable region, and this was expressed together with the full-length light chain to produce an anti-CD3 antibody as a TWO arm antibody, and the anti-CD3 antibody was purified from the culture supernatant.

Table 6 shows the antibody concentrations. When the extracellular domain of CD3ε was fused, the concentration after purification was decreased compared to the other variants, and this suggested that the expression level is low.

TABLE 6 Concentration Antibody name (mg/mL) hCE115HA/GLS One arm 0.808 hCE115HAGS/GLS One arm 1.580 hCE115HA/GLSGS One arm 0.756 hCE115HA-CD3/GLS One arm 0.379 hCE115HA-CD3_Linker/GLS One arm 0.441 hCE115HA/GLS-CD3 One arm 0.048 hCE115HA/GLS-CD3_Linker One arm 0.056

Example 7: Evaluation of CD3ε-Binding Activity of Protease-Treated Anti-CD3 Antibody Derivatives with Masked Binding to CD3ε and of Noncleavable Antibodies

The antibodies prepared in Example 6 were subjected to protease treatment, and whether the anti-CD3 antibody derivatives with masked binding to CD3ε bind to CD3ε was assessed. The antibodies were obtained by the method shown in Reference Example 2, uPA (Recombinant Human u-Plasminogen Activator, R&D systems) was added at a final concentration of 25 nM to 5 μg of the obtained antibodies, and the mixture was reacted in PBS at 37° C. for 16 hours to 20 hours.

The CD3ε extracellular domain (CD3ε homodimer) was biotinylated using No-Weigh Premeasured NHS-PEO4-Biotin Microtubes (Pierce) according to the protocol. A blocking buffer (0.5× Block ACE containing 0.02% Tween20 and 0.05% ProClin300) was used to dilute the antigens, beads, and antibodies. The biotinylated antigens and paramagnetic beads (Dynabeads (registered trademark) MyOne™ Streptavidin T1, Invitrogen) were mixed and allowed to stand at room temperature for ten minutes. At the same time, paramagnetic beads and blocking buffer were added to wells with no addition of antigens. The antibody solution treated or untreated with the protease was diluted to 4 μg/mL, 1 μg/mL, 0.25 μg/mL, 0.0625 μg/mL, 0.015625 μg/mL, and 0 μg/mL using PBS, and each of them was added in 25-μL aliquots. For the AN121 variant, 1 μg/mL was used as the highest dose. The beads and antibodies were mixed well, and then left to stand at room temperature for 30 minutes. After washing once with TBS (TaKaRa) containing 0.05% Tween20 (Nacalai), HRP-labeled anti-Kappa chain antibody (Anti-Human Kappa Chain antibody, Abcam, ab79115) diluted 16000-times was added and the resulting mixture was allowed to stand at room temperature for another ten minutes. The mixture was washed again three times, and Lumi-Phos-HRP (Lucmigen, PAA457009) was added thereto as a substrate. After allowing the mixture to stand at room temperature for two minutes, luminescence was detected on Synergy HTX. The detected luminescence values were presented as ratios to the values for the respective wells containing the same concentration of the antibody and no antigen. The results are shown in FIG. 8. As shown in FIG. 8, antibodies that do not contain a cancer tissue-specific protease-cleavable linker (β) did not show any variation in binding activity between the case where the protease was added (protease-treated) and the case where the protease was not added (protease-untreated). In contrast, antibodies containing a cancer tissue-specific protease-cleavable linker (β) showed a remarkable increase in the binding to CD3ε by the protease treatment. Specifically, when a cancer tissue-specific protease-cleavable linker (β) was connected to the heavy chain, as indicated by hCE115HAuPA04, the change in binding activity before and after cleavage was the greatest under the conditions that the masking molecule (γ) consisted of seven amino acids, the cancer tissue-specific protease-cleavable linker (β) contained a GS linker composed of a repetition of GGGS and an uPA cleavable sequence, and the linker was linked to the heavy chain N terminus via the GGGS peptide sequence. On the other hand, when the masking molecule (γ) was composed of 20 amino acids (hCE115HAuPA20) or 27 amino acids (hCE115HAuPA27), the binding activity increase rate due to the protease treatment was decreased as compared to that obtained using the masking molecule (γ)composed of seven amino acids (hCE115HAuPAO4). The result of linking a masking molecule (γ) and a cancer tissue-specific protease-cleavable linker (β) to the AN121 heavy chain is shown in (iv) of FIG. 8, and indicates that, similarly to the results indicated for hCE115HA, cleavage by the protease increased CD3 binding activity. Regarding AN121 as well, the short masking molecule (γ) was shown to be more preferable to the masking molecule (γ) composed of 20 amino acids (ANuPA20) or 27 amino acids (ANuPA27). Similarly, when a cancer tissue-specific protease-cleavable linker (β) was connected to the light chain, as shown by GLSuPA04, the change in the binding activity before and after cleavage was the greatest under the conditions that the masking molecule (γ) consisted of seven amino acids, the cancer tissue-specific protease-cleavable linker (β) contained a GS linker composed of a repetition of GGGS and an uPA cleavable sequence, and the linker was linked to the heavy chain N terminus via the GGGS peptide sequence. On the other hand, when the masking molecule (γ) was composed of 20 amino acids (GLSuPA20) or 27 amino acids (GLSuPA27), the binding activity increase rate due to the protease treatment was decreased as compared that obtained using the masking molecule (γ)composed of seven amino acids (GLSuPA04).

This examination revealed that a naturally-occurring sequence can be used as the masking molecule (γ), and it was shown that molecules exhibiting desired effects can be prepared by changing the length of the masking molecule (γ) in line with a naturally-occurring sequence as in the method indicated in the present Example so that the masking molecule (γ) will have an appropriate length and by changing the length of the cancer tissue-specific protease-cleavable linker (β).

Example 8: Evaluation of CD3ε-Binding Activity of Protease-Treated Anti-CD3 Antibody Derivatives with Masked Binding to CD3ε and of Noncleavable Antibodies

In Example 7, sequences were cleaved using uPA, but it is known that the sequences can also be cleaved by matriptase. Accordingly, whether the samples prepared in Example 7 were also cleaved by matriptase and bound to CD3 was assessed. Antibodies were prepared by the method of Example 7, and then human MT-SP1 (Matriptase/ST14 Catalytic Domain, R&D systems) was added at a final concentration of 50 nM to 3 μg of each of the antibodies. After addition, the respective mixture was incubated at 37° C. for 22 hours, and then binding activities were assessed in the same manner as in Example 7. The results are shown in FIG. 9. As shown in FIG. 9, antibodies that do not contain a cancer tissue-specific protease-cleavable linker (β) did not show any variation in binding activity between the case where the protease was added (protease-treated) and the case where the protease was not added (protease-untreated). In contrast, antibodies containing a cancer tissue-specific protease-cleavable linker (β) showed a remarkable increase in the binding to CD3ε through by the protease treatment. Specifically, when a cancer tissue-specific protease-cleavable linker (β) was connected to the heavy chain, as indicated by hCE115HAuPA04, the change in binding activity before and after cleavage was the greatest under the conditions that the masking molecule (γ) consisted of seven amino acids, the cancer tissue-specific protease-cleavable linker (β) contained a GS linker composed of a repetition of GGGS and an uPA cleavable sequence, and the linker was linked to the heavy chain N terminus by the GGGS peptide sequence. On the other hand, when the masking molecule (γ) was composed of 20 amino acids (hCE115HAuPA20) or 27 amino acids (hCE115HAuPA27), the binding activity increase rate due to the protease treatment was decreased as compared to that obtained using the masking molecule (γ)composed of seven amino acids (hCE115HAuPAO4). Similarly, when a cancer tissue-specific protease-cleavable linker (13) was connected to the light chain, as shown by GLSuPA04, the change in the binding activity before and after cleavage was the greatest under the conditions that the masking molecule (γ) consisted of seven amino acids, the cancer tissue-specific protease-cleavable linker (13) contained a GS linker composed of a repetition of GGGS and an uPA cleavable sequence, and the linker was linked to the heavy chain N terminus by the GGGS peptide sequence. On the other hand, when the masking molecule (γ) was composed of 20 amino acids (GLSuPA20) or 27 amino acids (GLSuPA27), the binding activity increase rate due to the protease treatment was decreased as compared to that obtained using the masking molecule (γ)composed of seven amino acids (GLSuPA04). This result was similar to the result shown in Example 7, indicating that the protease used to carry out the cleavage is not limited to uPA and may be other proteases.

Example 9: Evaluation of CD3ε-Binding Activity of Protease-Treated Anti-CD3 Antibody Derivatives with Masked Binding to CD3ε and of Noncleavable Antibodies

In Examples 7 and 8, a sequence (LSGRSDNH; SEQ ID NO: 47) reported in WO2013/163631 was used and cleavage was carried out using uPA or matriptase (MT-SP1). Next, whether the binding activity is increased by protease treatment, as in the case with uPA and MT-SP1, when using a sequence cleaved by MMP-2 as shown in Example 3, was examined. Antibodies were prepared by a method similar to that of Example 7.

MMP-2 (R&D systems) was preliminarily activated by adding a 100-mM solution of 4-aminophenylmercuric acetate (APMA, SIGMA) in dimethylsulfoxide (DMSO, Junsei Chemical Co., Ltd.) to MMP-2 at 1/100 equivalents (by volume), and then incubating the mixture at 37° C. for two hours. Activated MMP-2 was added at a final concentration of 50 nM to 3 μg of each of the antibodies, and the respective mixture was reacted at 37° C. for 22 hours. During incubation, the mixture was adjusted so that TBS (TaKaRa) supplemented with 0.1% Tween20 and 10 mM CaCl₂ accounts for half of the overall volume. After incubation, binding was evaluated by the electrochemical luminescence (ECL) method. The human CD3ε homodimer protein to which biotin had been added (18 pmol/mL or 0 pmol/mL), the antibody solutions prepared at 1 μg/mL, 0.25 μg/mL, 0.0625 μg/mL, 0.015625 μg/mL, or 0 μg/mL, and anti-human Kappa chain antibody labeled with sulfo-tag (Ru complex) (SouthemBiotech, 2.7 μg/mL) were added to each well of Nunc-Immuno™ MicroWell™ 96 well round plates (Nunc) in 25-μL aliquots, and after mixing, the plates were incubated at room temperature for one hour or more to form antibody-antigen complexes. TBST containing 0.5% BSA (TBS (TaKaRa) solution containing 0.1% Tween20), referred to as the blocking solution, was added at 150 μL aliquots to each well of a streptavidin plate (MSD), and the plate was incubated at room temperature for two hours or more. The blocking solution was removed, and then the plate was washed three times with 250 μL of TBS(+) solution containing 0.1% Tween20. The antibody-antigen complex solution was added at 50-μL aliquots to each well, and the plate was shaken at 700 rpm at room temperature for one hour to bind the antibody-antigen complexes to the streptavidin plate. After removing the antibody-antigen complex solution, 2×READ buffer (MSD) was added at 150-μL aliquots to each well, and the luminescent signal from the sulfo-tag was detected using Sector Imager 2400 (MSD). The results are shown in FIG. 10.

As shown in FIG. 10, the antibodies that do not contain a cancer tissue-specific protease-cleavable linker (β) did not show any variation in binding activity between the case where the protease was added (protease-treated) and the case where the protease was not added (protease-untreated). In contrast, the antibody (hCE115HAMMP02) containing a cancer tissue-specific protease-cleavable linker (β) showed a remarkable increase in binding to CD3ε by the protease treatment. Even when a cancer tissue-specific protease-cleavable linker (β) was connected to the light chain, binding to CD3ε increased similarly. As described in Example 3, a longer linker may be used when connecting to a light chain; however, it was revealed that at least the use of the GGGGSPLSLAGGGS (SEQ ID NO: 55) sequence shown in the present Example exhibited the desired effects. The foregoing indicated that not only the cancer tissue-specific protease-cleavable linkers (β) indicated in Examples 7 and 8, but also the cancer tissue-specific protease-cleavable linkers (β) of Example 3 shown in the present Example can be used.

Example 10: Evaluation of CD3 Activation of Protease-Treated Anti-CD3 Antibody Derivatives with Masked Binding to CD3ε and of Noncleavable Antibodies

In Examples 7 to 9, it was revealed that antibodies with masked binding to CD3ε showed a remarkable increase in binding to CD3ε by protease treatment. Next, whether activity of CD3 can be induced by protease treatment of antibodies was assessed. SK-pca-60 cells which correspond to SK-HEP1 cells that forcibly express GPC3 were used as target cells, and NFAT-RE-luc2-Jurkat cells (Promega) were used as effector cells. NFAT-RE-luc2-Jurkat cells (Promega) are derived from a human leukemia T-cell line, and are cells that have been modified to express luciferase in response to NFAT with CD3 activation. The anti-CD3 antibodies shown in Table 7 and GCH065-F760mnN17 (heavy chain SEQ ID NO: 112 and light chain SEQ ID NO: 113) were prepared according to the method of Reference Example 2. Furthermore, to prepare bispecific antibodies, the respective purified homodimers were used to prepare a desired bispecific antibody in which one of the Fab domains binds to GPC3 and the other Fab domain binds to CD3in accordance with a method known to those skilled in the art (International Publication No. WO2015/046467). The bispecific antibody was written as XX/YY//ZZ, where XX indicates the anti-CD3 antibody heavy chain variable region, YY indicates the anti-CD3 antibody light chain variable region, and ZZ indicates the anti-GPC3 antibody. Then, protease treatment was carried out as in Example 7. For protease treatment, uPA (Recombinant Human u-Plasminogen Activator, R&D systems) was added at a final concentration of 25 nM to an antibody, and the mixture was reacted in PBS at 37° C. for twelve hours or more. Furthermore, antibodies not treated with protease were also incubated, similarly to the protease-treated antibody, at 37° C. for the same duration.

A 25-μL aliquot of the protease-treated antibody solution or protease-untreated antibody solution were added to 50 μL of a cell solution prepared by mixing NFAT-RE-luc2-Jurkat cells (Promega) (7.5×10⁴ cells per well) and SK-pca-60 cells (1.25×10⁴ cells per well) which correspond to SK-HEP1 cells forcibly expressing GPC3, and, 24 hours later, luciferase activity was measured using Bio-Glo Luciferase assay system (Promega, G7941). Luciferase activity was measured using 2104 EnVision (Perkin Elmer), the increase rate was calculated from the obtained luminescence value by defining the result from wells without antibody addition as 1, and the results are shown in FIGS. 11 to 15. Furthermore, the increase rates due to the protease treatment (value obtained by dividing the increase rate in the luminescence value of a protease-treated antibody by the increase rate in the luminescence value of a protease-untreated antibody) are shown in Table 8.

As indicated in (i) of FIGS. 11 to 15, CD3 activation was observed with unmodified antibodies; however, CD3 activation was not observed with antibodies to which the masking molecule (γ) was attached using a linker sequence that is not cleavable by proteases. On the other hand, as indicated in (ii) of FIGS. 11 to 15, higher CD3 activation than before protease cleavage was observed for protease-treated antibodies to which the masking molecule (γ) was attached using a cancer tissue-specific protease-cleavable linker (β). Specifically, when a cancer tissue-specific protease-cleavable linker (β) was connected to the heavy chain, as indicated by hCE115HAuPA04, the change in CD3 activation before and after cleavage was the greatest under the conditions that the masking molecule (γ) consisted of seven amino acids, the cancer tissue-specific protease-cleavable linker (β) contained a GS linker composed of a repetition of GGGS and an uPA cleavable sequence, and the linker was linked to the heavy chain N terminus via the GGGS peptide sequence. The next largest amount of change was observed for the sequences in which the masking molecule (γ) was composed of 20 amino acids (hCE115HAuPA20, ANuPA20). When the masking molecule (γ) was composed of 27 amino acids (hCE115HAuPA27, ANuPA27), the increase rate in CD3 activation due to the protease treatment was remarkably decreased compared to the case where the masking molecule (γ) was composed of seven amino acids (hCE115HAuPAO4). Similarly, when a cancer tissue-specific protease-cleavable linker (β) was connected to the light chain, as indicated by GLSuPA04, the change in CD3 activation before and after cleavage was the greatest under the conditions that the masking molecule (γ) consisted of seven amino acids, the cancer tissue-specific protease-cleavable linker (β) contained a GS linker composed of a repetition of GGGS and an uPA cleavable sequence, and the linker was linked to the heavy chain N terminus via the GGGS peptide sequence. The next largest amount of change was observed for the sequence in which the masking molecule (γ) was composed of 20 amino acids (GLSuPA20). When the masking molecule (γ) was composed of 27 amino acids (GLSuPA27), the increase rate in CD3 activation due to the protease treatment was decreased compared to the case where the masking molecule (γ) was composed of seven amino acids (GLSuPA04).

Examples 6 to 10 demonstrated that antibodies comprising a masking molecule (γ) having a naturally-occurring amino acid sequence and a cancer tissue-specific protease-cleavable linker (β) bound to the antigen in a protease-dependent manner, and activated CD3 by binding to CD3. This study revealed that a naturally-occurring sequence can be used as the masking molecule (γ), and showed that molecules exhibiting desired effects can be prepared by changing the length of the masking molecule (γ) according to a naturally-occurring sequence so that it will have an appropriate length as in the method indicated in the present Examples, or by changing the length of the linker. Besides the sequences used in the present Examples, those available as the cancer tissue-specific protease-cleavable linker (β) are described in JBC, Aug. 15, 1997, vol. 272, no. 33, 20456-20462; Proteomics 2005, 5, 1292-1298; Biochem. J. (2010) 426, 219-228; and WO2015/116933. Furthermore, an 8-amino-acid peptide sequences in which X1X2X3X4X5X6X7X8 are aligned as shown in Table 9 may also be used.

TABLE 9 Amino acid used Amino acid at Position this time each position X1: L YWFMAQNEK X2: S WFAPQED X3: G YWFILMPTQNHC X4: R YWFIMPQNEDK X5: S WILMAGQNEDKRH X6: D WFMPSQKRC X7: N YWFLVMAGPC X8: H WFIAGPTQEDKC

INDUSTRIAL APPLICABILITY

The multiple antigen-binding molecule fusion molecules of the present invention can be used in reagents for experimental studies, pharmaceuticals, and such.

According to the present invention, due to the binding of a masking molecule (γ) to a multiple antigen-binding molecule (α) via a cancer tissue-specific protease-cleavable linker (β), immune cells are not readily recruited to normal tissues, which provides an effect of reducing side effects caused by the multiple antigen-binding molecule (α), and therefore, the multiple antigen-binding molecule fusion molecules of the present invention are particularly useful as pharmaceuticals. 

1. A multiple antigen-binding molecule fusion molecule comprising: a multiple antigen-binding molecule (α) which comprises an immune cell antigen-binding region which recognizes an antigen that comprises a polypeptide consisting of the amino acid sequence QDGNE (SEQ ID NO: 15) and a cancer antigen-binding region which recognizes a cancer antigen; a cancer tissue-specific protease-cleavable linker (β) which comprises a polypeptide consisting of a target sequence of a cancer tissue-specific protease; and a masking molecule (γ) which comprises a polypeptide consisting of the amino acid sequence QDGNE (SEQ ID NO: 15); wherein the multiple antigen-binding molecule (α) and the masking molecule (γ) are linked via the cancer tissue-specific protease-cleavable linker (β).
 2. The multiple antigen-binding molecule fusion molecule of claim 1, wherein the immune cell antigen-binding region recognizes at least one type of immune cell antigen other than the antigen that comprises a polypeptide consisting of the amino acid sequence QDGNE (SEQ ID NO: 15).
 3. The multiple antigen-binding molecule fusion molecule of claim 2, wherein the immune cell antigen-binding region does not recognize two or more immune cell antigens simultaneously.
 4. The multiple antigen-binding molecule fusion molecule of any one of claims 1 to 3, wherein the multiple antigen-binding molecule (α) is an antibody or an antibody fragment comprising at least two Fv regions, and the cancer antigen-binding region and the immune cell antigen-binding region are formed by different Fv regions.
 5. The multiple antigen-binding molecule fusion molecule of claim 4, wherein light chains of the antibody or the antibody fragment comprising at least two Fv regions both comprise a same amino acid sequence.
 6. The multiple antigen-binding molecule fusion molecule of claim 4 or 5, wherein the antibody or antibody fragment comprising at least two Fv regions further comprises an Fc region, and the Fc region is modified so as to lack a function of recognizing an Fcγ receptor.
 7. The multiple antigen-binding molecule fusion molecule of any one of claims 4 to 6, wherein the cancer tissue-specific protease-cleavable linker (β) is fused to a heavy chain N-terminus or a light chain N-terminus of the Fv region that forms the immune cell antigen-binding region.
 8. The multiple antigen-binding molecule fusion molecule of claim 7, wherein the cancer tissue-specific protease-cleavable linker (β) and the masking molecule (γ) form a linear fusion polypeptide, and wherein the number of amino acids in the fusion polypeptide is eleven or more to 65 or less when the cancer tissue-specific protease-cleavable linker (β) is fused to the heavy chain N-terminus of the Fv region that forms the immune cell antigen-binding region; and the number of amino acids in the fusion polypeptide is 16 or more to 65 or less when the cancer tissue-specific protease-cleavable linker (β) is fused to the light chain N terminus of the Fv region that forms the immune cell antigen-binding region.
 9. The multiple antigen-binding molecule fusion molecule of any one of claims 1 to 8, wherein the target sequence is the amino acid sequence PLGLAG (SEQ ID NO: 9).
 10. A pharmaceutical composition which comprises the multiple antigen-binding molecule fusion molecule of any one of claims 1 to 9 and a pharmaceutically acceptable carrier.
 11. The pharmaceutical composition of claim 10, which is for treating cancer.
 12. A method for treating cancer, wherein the method comprises administering the pharmaceutical composition of claim 10 or 11 to a patient.
 13. A method for identifying a linear epitope, wherein the method comprises identifying a linear epitope comprised in the immune cell antigen and recognized by the immune cell antigen-binding region based on three-dimensional protein structure analysis data obtained by using a protein complex of an immune cell antigen and an immune cell antigen-binding region which recognizes the immune cell antigen.
 14. A method for producing a multiple antigen-binding molecule fusion molecule, wherein the method comprises expressing a fusion protein in which a linear epitope is fused to a multiple antigen-binding molecule (α) which comprises a cancer antigen-binding region that recognizes a cancer antigen and an immune cell antigen-binding region that recognizes an immune cell antigen via a cancer tissue-specific protease-cleavable linker (β) which comprises a region that is cleavable by a protease specifically expressed in a cancer tissue expressing the cancer antigen. 